Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins)

sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands
characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies

Lineage:

1. Root: scop
2. Class: All beta proteins [48724]
3. Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) [88632]
   sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands
   characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies

Superfamilies:

1. Nucleoplasmin-like core domain [69203] (1)
   oligomerizes into a pentameric ring structure
   uperfamily
   1. Nucleoplasmin-like core domain [69204] (3)
      1. Nucleoplasmin core [69205]
         1. Xenopus laevis [TaxId: 8355] [69206] (1)
            1. 1k5j
               mutant
               1. chain a [68201]
               2. chain b [68202]
               3. chain c [68203]
               4. chain d [68204]
               5. chain e [68205]
      2. Chromatin decondensation protein 1 (Crp1, Nlp) [89223]
         1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89224] (1)
            1. 1nlq
               complexed with mg
               1. chain a [85853]
               2. chain b [85854]
               3. chain c [85855]
               4. chain d [85856]
               5. chain e [85857]
      3. Nucleophosmin (NO38) [117086]
         1. African clawed frog (Xenopus laevis) [TaxId: 8355] [117087] (2)
            SQ P07222 16-122
            1. 1xe0
               1. chain a [115197]
               2. chain b [115198]
               3. chain c [115199]
               4. chain d [115200]
               5. chain e [115201]
               6. chain f [115202]
               7. chain g [115203]
               8. chain h [115204]
               9. chain i [115205]
               10. chain j [115206]
            2. 1xb9
               1. chain a [115066]
               2. chain b [115067]
               3. chain c [115068]
               4. chain d [115069]
               5. chain e [115070]
               6. chain f [115071]
               7. chain g [115072]
               8. chain h [115073]
               9. chain i [115074]
               10. chain j [115075]
2. Positive stranded ssRNA viruses [88633] (9)
   uperfamily
   1. Picornaviridae-like VP (VP1, VP2, VP3 and VP4) [88634] (18)
      the order of the chains N-VP0-VP3-VP1-C is as in the polyprotein; VP0 is cleaved later upon capsid assembly to VP4 and VP2
      there is a different order in the shuffled genome of insect picorna-like proteins (Cricket paralysis virus)
      1. Human enterovirus B coat proteins [88635]
         1. Human coxsackievirus B3 [TaxId: 12072] [49681] (1)
            1. 1cov
               complexed with myr, plm
               1. chain 4,2 [83045]
               2. chain 3 [23566]
               3. chain 1 [23564]
         2. Human coxsackievirus A9 [TaxId: 12067] [49683] (1)
            1. 1d4m
               1. chain 4,2 [83046]
               2. chain 3 [23569]
               3. chain 1 [23567]
         3. Human echovirus 1 [TaxId: 46633] [49685] (1)
            1. 1ev1
               complexed with myr, plm
               1. chain 4,2 [83050]
               2. chain 3 [23572]
               3. chain 1 [23570]
         4. Human echovirus 11 [TaxId: 12078] [74890] (4)
            1. 1h8t
               complexed with doa, myr
               1. chain d,b [83061]
               2. chain c [70922]
               3. chain a [70920]
            2. 2c8i
               automatically matched to d1h8ta_
               1. region a:1-289 [130103]
            3. 2c8i
               automatically matched to d1h8tc_
               1. region c:1-238 [130104]
            4. 1upn
               1. chain d,b [99761]
               2. chain c [99763]
               3. chain a [99762]
      2. Bovine enterovirus coat proteins [49676]
         1. Bovine enterovirus, VG-5-27 [TaxId: 12064] [49677] (1)
            1. 1bev
               complexed with myr, so4
               1. chain 4,2 [83040]
               2. chain 3 [23557]
               3. chain 1 [23555]
      3. Poliovirus coat proteins [49666]
         1. Poliovirus type 1, strain Mahoney [TaxId: 12080] [49667] (12)
            1. 1hxs
               complexed with myr, plm
               1. chain 4,2 [83073]
               2. chain 3 [65954]
               3. chain 1 [65952]
            2. 1ar7
               complexed with myr, sph; mutant
               1. chain 4,2 [83032]
               2. chain 3 [23389]
               3. chain 1 [23387]
            3. 1po1
               complexed with j80, myr
               1. chain 4,2 [83102]
               2. chain 3 [23398]
               3. chain 1 [23396]
            4. 1al2
               complexed with myr, sph; mutant
               1. chain 4,2 [83030]
               2. chain 3 [23392]
               3. chain 1 [23390]
            5. 1ar9
               complexed with myr, sph; mutant
               1. chain 4,2 [83034]
               2. chain 3 [23395]
               3. chain 1 [23393]
            6. 1po2
               complexed with j77, myr
               1. chain 4,2 [83103]
               2. chain 3 [23401]
               3. chain 1 [23399]
            7. 1asj
               complexed with myr, sph
               1. chain 4,2 [83035]
               2. chain 3 [23404]
               3. chain 1 [23402]
            8. 1ar6
               complexed with myr, sph; mutant
               1. chain 4,2 [83031]
               2. chain 3 [23407]
               3. chain 1 [23405]
            9. 2plv
               complexed with myr, sph
               1. chain 4,2 [83137]
               2. chain 3 [23386]
               3. chain 1 [23384]
            10. 1ar8
                complexed with myr, sph; mutant
                1. chain 4,2 [83033]
                2. chain 3 [23410]
                3. chain 1 [23408]
            11. 1pov
                contains unprocessed VP0
                complexed with myr, sph
                1. chain 0 [23411]
                2. chain 3 [23413]
                3. chain 1 [23412]
            12. 1xyr
                automatically matched to d1pov1_
                1. region 1:71-302 [122460]
         2. Poliovirus type 2, strain Lansing [TaxId: 12083] [49668] (1)
            1. 1eah
               complexed with myr, sc4
               1. chain 4,2 [83047]
               2. chain 3 [23416]
               3. chain 1 [23414]
         3. Poliovirus type 3, strain Sabin [TaxId: 12086] [49669] (7)
            1. 1pvc
               complexed with myr, sph
               1. chain 4,2 [83104]
               2. chain 3 [23419]
               3. chain 1 [23417]
            2. 1vbb
               complexed with j80, myr
               1. chain 4,2 [83126]
               2. chain 3 [23422]
               3. chain 1 [23420]
            3. 1vbc
               complexed with j77, myr
               1. chain 4,2 [83127]
               2. chain 3 [23425]
               3. chain 1 [23423]
            4. 1vbe
               complexed with j78, myr; mutant
               1. chain 4,2 [83129]
               2. chain 3 [23431]
               3. chain 1 [23429]
            5. 1vbd
               complexed with j78, myr
               1. chain 4,2 [83128]
               2. chain 3 [23428]
               3. chain 1 [23426]
            6. 1vba
               complexed with j78, myr
               1. chain 4,2 [83125]
               2. chain 3 [23434]
               3. chain 1 [23432]
            7. 1piv
               complexed with myr, w71
               1. chain 4,2 [83101]
               2. chain 3 [23437]
               3. chain 1 [23435]
      4. Rhinovirus coat proteins [49670]
         1. Human rhinovirus B 14 (HRV-14) [TaxId: 12131] [49671] (30)
            1. 1ncq
               complexed with w11
               1. chain d,b [91802]
               2. chain c [91804]
               3. chain a [91803]
            2. 1k5m
               grafted HIV-1 v3 loop in chain B
               complexed with sph
               1. chain d,b [83093]
               2. chain c [72080]
               3. chain a [72078]
            3. 4rhv
               1. chain 4,2 [83147]
               2. chain 3 [23440]
               3. chain 1 [23438]
            4. 1na1
               complexed with w11
               1. chain d,b [91742]
               2. chain c [91744]
               3. chain a [91743]
            5. 1rud
               complexed with w84; mutant
               1. chain 4,2 [83115]
               2. chain 3 [23446]
               3. chain 1 [23444]
            6. 1r09
               complexed with dms, jen
               1. chain 4,2 [83110]
               2. chain 3 [23443]
               3. chain 1 [23441]
            7. 1vrh
               complexed with sd8; mutant
               1. chain 4,2 [83130]
               2. chain 3 [23467]
               3. chain 1 [23465]
            8. 2rr1
               complexed with w8r
               1. chain 4,2 [83143]
               2. chain 3 [23455]
               3. chain 1 [23453]
            9. 2r07
               complexed with w33
               1. chain 4,2 [83140]
               2. chain 3 [23449]
               3. chain 1 [23447]
            10. 2rs1
                complexed with w84
                1. chain 4,2 [83144]
                2. chain 3 [23458]
                3. chain 1 [23456]
            11. 1rui
                complexed with w84; mutant
                1. chain 4,2 [83120]
                2. chain 3 [23464]
                3. chain 1 [23462]
            12. 1ruf
                mutant
                1. chain 4,2 [83117]
                2. chain 3 [23473]
                3. chain 1 [23471]
            13. 1rue
                complexed with w35; mutant
                1. chain 4,2 [83116]
                2. chain 3 [23470]
                3. chain 1 [23468]
            14. 2rm2
                complexed with w43
                1. chain 4,2 [83141]
                2. chain 3 [23452]
                3. chain 1 [23450]
            15. 1ruh
                complexed with w84; mutant
                1. chain 4,2 [83119]
                2. chain 3 [23461]
                3. chain 1 [23459]
            16. 1hrv
                complexed with sdz
                1. chain 4,2 [83063]
                2. chain 3 [23479]
                3. chain 1 [23477]
            17. 1ruj
                mutant
                1. chain 4,2 [83121]
                2. chain 3 [23500]
                3. chain 1 [23498]
            18. 2rmu
                mutant
                1. chain 4,2 [83142]
                2. chain 3 [23503]
                3. chain 1 [23501]
            19. 1rmu
                complexed with trs; mutant
                1. chain 4,2 [83113]
                2. chain 3 [23506]
                3. chain 1 [23504]
            20. 1hri
                complexed with s57
                1. chain 4,2 [83062]
                2. chain 3 [23476]
                3. chain 1 [23474]
            21. 2r06
                complexed with w35
                1. chain 4,2 [83139]
                2. chain 3 [23494]
                3. chain 1 [23492]
            22. 1rug
                complexed with w35; mutant
                1. chain 4,2 [83118]
                2. chain 3 [23497]
                3. chain 1 [23495]
            23. 2hwb
                complexed with w91; mutant
                1. chain 4,2 [83131]
                2. chain 3 [23509]
                3. chain 1 [23507]
            24. 2r04
                complexed with w71
                1. chain 4,2 [83138]
                2. chain 3 [23488]
                3. chain 1 [23486]
            25. 2rs5
                complexed with w56
                1. chain 4,2 [83146]
                2. chain 3 [23491]
                3. chain 1 [23489]
            26. 2hwc
                complexed with w54; mutant
                1. chain 4,2 [83132]
                2. chain 3 [23512]
                3. chain 1 [23510]
            27. 2rs3
                complexed with w59
                1. chain 4,2 [83145]
                2. chain 3 [23482]
                3. chain 1 [23480]
            28. 1r08
                complexed with w42
                1. chain 4,2 [83109]
                2. chain 3 [23485]
                3. chain 1 [23483]
            29. 1ruc
                complexed with w35; mutant
                1. chain 4,2 [83114]
                2. chain 3 [23515]
                3. chain 1 [23513]
            30. 1rvf
                1. chain 4,2 [83122]
                2. chain 3 [23518]
                3. chain 1 [23516]
         2. Human rhinovirus 16, (HRV-16) [TaxId: 31708] [49672] (9)
            1. 1aym
               complexed with dao, myr, zn; mutant
               1. chain 4,2 [83036]
               2. chain 3 [23521]
               3. chain 1 [23519]
            2. 1nd2
               complexed with myr, zn
               1. chain d,b [91809]
               2. chain c [91811]
               3. chain a [91810]
            3. 1qju
               complexed with myr, w01, zn; mutant
               1. chain 4,2 [83105]
               2. chain 3 [23524]
               3. chain 1 [23522]
            4. 1ncr
               complexed with myr, w11, zn
               1. chain d,b [91805]
               2. chain c [91807]
               3. chain a [91806]
            5. 1qjy
               complexed with myr, w03, zn; mutant
               1. chain 4,2 [83107]
               2. chain 3 [23527]
               3. chain 1 [23525]
            6. 1c8m
               complexed with w11, zn
               1. chain 4,2 [83044]
               2. chain 3 [23530]
               3. chain 1 [23528]
            7. 1ayn
               complexed with dao, myr, zn; mutant
               1. chain 4,2 [83037]
               2. chain 3 [23536]
               3. chain 1 [23534]
            8. 1nd3
               complexed with w11, zn
               1. chain d,b [91812]
               2. chain c [91814]
               3. chain a [91813]
            9. 1qjx
               complexed with myr, w02, zn; mutant
               1. chain 4,2 [83106]
               2. chain 3 [23533]
               3. chain 1 [23531]
         3. Human rhinovirus A 1A (HRV-1A) [TaxId: 12134] [49673] (4)
            1. 1r1a
               complexed with suc
               1. chain 4,2 [83111]
               2. chain 3 [23539]
               3. chain 1 [23537]
            2. 2hwd
               complexed with w91
               1. chain 4,2 [83133]
               2. chain 3 [23542]
               3. chain 1 [23540]
            3. 2hwf
               complexed with jen
               1. chain 4,2 [83135]
               2. chain 3 [23548]
               3. chain 1 [23546]
            4. 2hwe
               complexed with w54
               1. chain 4,2 [83134]
               2. chain 3 [23545]
               3. chain 1 [23543]
         4. Human rhinovirus A 2 (HRV-2) [TaxId: 12130] [49674] (2)
            1. 1fpn
               complexed with dao
               1. chain 4,2 [83053]
               2. chain 3 [23551]
               3. chain 1 [23549]
            2. 1v9u
               complexed with ca, dao
               1. chain 4,2 [100550]
               2. chain 3 [100552]
               3. chain 1 [100551]
         5. Human rhinovirus 3, (HRV-3) [TaxId: 44130] [49675] (1)
            1. 1rhi
               complexed with ca
               1. chain 4,2 [83112]
               2. chain 3 [23554]
               3. chain 1 [23552]
      5. Aphthovirus (Foot-and-mouth disease virus) coat proteins [49659]
         1. FMDV (Foot-and-mouth disease virus), strain bfs, 1860 [TaxId: 12110] [49660] (4)
            1. 1qqp
               complexed with idu, sgn
               1. chain 4,2 [83108]
               2. chain 3 [23365]
               3. chain 1 [23363]
            2. 1bbt
               1. chain 4,2 [83039]
               2. chain 3 [23368]
               3. chain 1 [23366]
            3. 1fod
               1. chain 4,2 [83052]
               2. chain 3 [23371]
               3. chain 1 [23369]
            4. 1fmd
               1. chain 4,2 [83051]
               2. chain 3 [23374]
               3. chain 1 [23372]
      6. Theilovirus capsid proteins [49686]
         1. Theiler's murine encephalomyelitis virus, strain da [TaxId: 12124] [49687] (2)
            1. 1tme
               1. chain 4,2 [83123]
               2. chain 3 [23575]
               3. chain 1 [23573]
            2. 1tmf
               1. chain 4,2 [83124]
               2. chain 3 [23578]
               3. chain 1 [23576]
      7. Mengo encephalomyocarditis virus coat proteins [49678]
         1. Mengovirus [TaxId: 12107] [49679] (2)
            1. 2mev
               complexed with po4
               1. chain 4,2 [83136]
               2. chain 3 [23560]
               3. chain 1 [23558]
            2. 1mec
               complexed with po4
               1. chain 4,2 [83100]
               2. chain 3 [23563]
               3. chain 1 [23561]
      8. Swine vesicular disease virus coat proteins [89225]
         1. Swine vesicular disease virus [TaxId: 12075] [89226] (2)
            1. 1oop
               complexed with myr, sph
               1. chain d,b [87203]
               2. chain a [87204]
               3. chain c [87205]
            2. 1mqt
               complexed with spl
               1. chain d,b [91424]
               2. chain a [91425]
               3. chain c [91426]
      9. Insect picorna-like virus coat proteins [49654]
         different genetic order of VP segments due to extensive genome shuffling
         1. Cricket paralysis virus [TaxId: 12136] [49655] (1)
            1. 1b35
               1. chain b [23334]
               2. chain d,c [83038]
               3. chain a [23333]
   2. Comoviridae-like VP [88636] (3)
      duplication: mature coat protein consists of three similar domains that can be in a single chain or in two separate chains
      1. Nepovirus capsid protein [49629]
         duplication: cnosists of three very similar domains
         1. TRSV (Tobacco ringspot virus) [TaxId: 12282] [49630] (1)
            1. 1a6c
               1. region a:1-176 [23296]
               2. region a:177-348 [23297]
               3. region a:349-513 [23298]
      2. Comovirus coat proteins (VP37 and VP23) [49627]
         chain 1 is one-domain VP23; chain 2 is two-domain VP37
         1. CPMV (Cowpea mosaic virus) [TaxId: 12264] [89227] (4)
            1. 1ny7
               1. region 2:1-182 [86399]
               2. region 2:183-369 [86400]
               3. region 1:1-189 [86398]
            2. 2bfu
               automatically matched to d1ny721
               1. region l:1-182 [128453]
            3. 2bfu
               automatically matched to d1ny722
               1. region l:183-369 [128454]
            4. 2bfu
               automatically matched to d1ny711
               1. region s:1-189 [128455]
         2. BPMV (Bean pod mottle virus) [TaxId: 12260] [49628] (3)
            1. 1pgl
               1. region 2:1-182 [94691]
               2. region 2:183-370 [94692]
               3. region 1:1-185 [94690]
            2. 1pgw
               1. region 2:20-182 [94694]
               2. region 2:183-370 [94695]
               3. region 1:1-185 [94693]
            3. 1bmv
               1. region 2:3001-3182 [83042]
               2. region 2:2001-2189 [83043]
               3. region 1:1001-1185 [83041]
   3. Caliciviridae-like VP [88637] (1)
      1. Calicivirus capsid protein [63691]
         includes the P (protruding) domain of complex beta-structure containing a beta-barrel similar to the second domain of EF-TU
         1. Norwalk virus [TaxId: 11983] [63692] (1)
            1. 1ihm
               1. chain a [62385]
               2. chain b [62386]
               3. chain c [62387]
   4. Nodaviridae-like VP [88638] (3)
      1. Alphanodavirus capsid protein [49648]
         1. Black beetle virus [TaxId: 12285] [49649] (1)
            1. 2bbv
               protein/RNA complex; complexed with ca
               1. chain a [23323]
               2. chain b [23324]
               3. chain c [23325]
         2. Nodamura virus [TaxId: 12288] [49650] (1)
            1. 1nov
               1. chain a [23326]
               2. chain b [23327]
               3. chain c [23328]
         3. Pariacoto virus [TaxId: 103782] [49651] (1)
            1. 1f8v
               complexed with ca, so4
               1. chain a,d [23329]
               2. chain b,e [23330]
               3. chain c,f [23331]
   5. Tetraviridae-like VP [101568] (1)
      1. Tetraomegavirus capsid protein [101569]
         contains an insert beta-sandwich domain
         1. Nudaurelia capensis omega virus [TaxId: 12541] [101570] (1)
            1. 1ohf
               complexed with mg
               1. chain a [93014]
               2. chain b [93015]
               3. chain c [93016]
               4. chain d [93017]
   6. Bromoviridae-like VP [88639] (4)
      1. Cucumovirus coat protein [88640]
         1. CMV (Cucumber mosaic virus), strain fny [TaxId: 12305] [49646] (1)
            1. 1f15
               1. chain a [23320]
               2. chain b [23321]
               3. chain c [23322]
         2. TAV (Tomato aspermy virus) [TaxId: 12315] [82012] (1)
            1. 1laj
               complexed with mg, po4
               1. chain a [77865]
               2. chain b [77866]
               3. chain c [77867]
         3. BMV (Brome mosaic virus) [TaxId: 12302] [74886] (31)
            1. 1yc6
               automatically matched to d1js9b_
               1. region 1:36-189 [122911]
            2. 1yc6
               automatically matched to d1js9b_
               1. region 2:36-189 [122912]
            3. 1yc6
               automatically matched to d1js9b_
               1. region 3:36-189 [122913]
            4. 1yc6
               automatically matched to d1js9b_
               1. region 4:36-189 [122914]
            5. 1yc6
               automatically matched to d1js9b_
               1. region a:36-189 [122915]
            6. 1yc6
               automatically matched to d1js9b_
               1. region b:36-189 [122916]
            7. 1yc6
               automatically matched to d1js9b_
               1. region c:36-189 [122917]
            8. 1yc6
               automatically matched to d1js9b_
               1. region d:36-189 [122918]
            9. 1yc6
               automatically matched to d1js9b_
               1. region e:36-189 [122919]
            10. 1yc6
                automatically matched to d1js9b_
                1. region f:36-189 [122920]
            11. 1yc6
                automatically matched to d1js9b_
                1. region g:36-189 [122921]
            12. 1yc6
                automatically matched to d1js9b_
                1. region h:36-189 [122922]
            13. 1yc6
                automatically matched to d1js9b_
                1. region i:36-189 [122923]
            14. 1yc6
                automatically matched to d1js9b_
                1. region j:36-189 [122924]
            15. 1yc6
                automatically matched to d1js9b_
                1. region k:36-189 [122925]
            16. 1yc6
                automatically matched to d1js9b_
                1. region l:36-189 [122926]
            17. 1yc6
                automatically matched to d1js9b_
                1. region m:36-189 [122927]
            18. 1yc6
                automatically matched to d1js9b_
                1. region n:36-189 [122928]
            19. 1yc6
                automatically matched to d1js9b_
                1. region o:36-189 [122929]
            20. 1yc6
                automatically matched to d1js9b_
                1. region p:36-189 [122930]
            21. 1yc6
                automatically matched to d1js9b_
                1. region q:36-189 [122931]
            22. 1yc6
                automatically matched to d1js9b_
                1. region r:36-189 [122932]
            23. 1yc6
                automatically matched to d1js9b_
                1. region s:36-189 [122933]
            24. 1yc6
                automatically matched to d1js9b_
                1. region t:36-189 [122934]
            25. 1yc6
                automatically matched to d1js9b_
                1. region u:36-189 [122935]
            26. 1yc6
                automatically matched to d1js9b_
                1. region v:36-189 [122936]
            27. 1yc6
                automatically matched to d1js9b_
                1. region w:36-189 [122937]
            28. 1yc6
                automatically matched to d1js9b_
                1. region x:36-189 [122938]
            29. 1yc6
                automatically matched to d1js9b_
                1. region y:36-189 [122939]
            30. 1yc6
                automatically matched to d1js9b_
                1. region z:36-189 [122940]
            31. 1js9
                complexed with egl, mg
                1. chain a [71840]
                2. chain b [71841]
                3. chain c [71842]
         4. Cowpea chlorotic mottle virus [TaxId: 12303] [49636] (1)
            1. 1cwp
               protein/RNA complex
               1. chain a [23305]
               2. chain b [23306]
               3. chain c [23307]
   7. Tymoviridae-like VP [88641] (3)
      1. Tymovirus coat protein [88642]
         1. PHMV (Physalis mottle virus) [TaxId: 72539] [49642] (2)
            1. 1e57
               1. chain a [59259]
               2. chain b [59260]
               3. chain c [59261]
            2. 1qjz
               1. chain a [23314]
               2. chain b [23315]
               3. chain c [23316]
         2. DYMV (Desmodium yellow mottle tymovirus) [TaxId: 70821] [49644] (1)
            1. 1ddl
               1. chain a [23317]
               2. chain b [23318]
               3. chain c [23319]
         3. TYMV (Turnip yellow mosaic virus) [TaxId: 12154] [49640] (2)
            SQ P03608
            1. 1auy
               1. chain a [23311]
               2. chain b [23312]
               3. chain c [23313]
            2. 1w39
               1. chain a [109146]
               2. chain b [109147]
               3. chain c [109148]
   8. Tombusviridae-like VP [88643] (7)
      1. Necrovirus coat protein [49637]
         1. TNV (Tobacco necrosis virus) [TaxId: 12054] [49638] (1)
            1. 1c8n
               complexed with ca
               1. chain a [23308]
               2. chain b [23309]
               3. chain c [23310]
      2. Tombusvirus coat protein [49633]
         1. TBSV (Tomato bushy stunt virus) [TaxId: 12145] [49634] (1)
            1. 2tbv
               complexed with ca
               1. chain a [23302]
               2. chain b [23303]
               3. chain c [23304]
      3. Carmovirus coat protein [89228]
         1. CarMV (Carnation mottle virus) [TaxId: 11986] [89229] (1)
            1. 1opo
               complexed with ca, so4
               1. chain a [87240]
               2. chain b [87241]
               3. chain c [87242]
      4. Sobemovirus coat protein [88644]
         1. SMV (Sesbania mosaic virus) [TaxId: 12558] [49624] (7)
            SQ Q9EB06
            1. 1smv
               complexed with ca
               1. chain a [23288]
               2. chain b [23289]
               3. chain c [23290]
            2. 2vq0
               automatically matched to d1vaka_
               complexed with ca; mutant
               1. region a:73-268 [153422]
            3. 2vq0
               automatically matched to d1vaka_
               complexed with ca; mutant
               1. region b:73-268 [153423]
            4. 2vq0
               automatically matched to d1vaka_
               complexed with ca; mutant
               1. region c:73-268 [153424]
            5. 1vak
               deletion mutant
               1. chain a [113600]
            6. 1vb4
               deletion mutant
               1. chain a [113603]
            7. 1vb2
               deletion mutant
               1. chain a [113602]
         2. SBMV (Southern bean mosaic virus), cow pea strain [TaxId: 12139] [49632] (1)
            1. 4sbv
               complexed with ca
               1. chain a [23299]
               2. chain b [23300]
               3. chain c [23301]
         3. RYMV (Rice yellow mottle virus) [TaxId: 31744] [49626] (1)
            1. 1f2n
               complexed with ca
               1. chain a [23291]
               2. chain b [23292]
               3. chain c [23293]
         4. Cocksfoot mottle virus [TaxId: 40979] [82010] (1)
            1. 1ng0
               complexed with ca
               1. chain a [80475]
               2. chain b [80476]
               3. chain c [80477]
   9. Birnaviridae-like VP [141109] (1)
      dsRNA virus but unlike the other dsRNA viruses has a genomic arrangement and genomic replication strategy similar to +sRNA viruses; includes Pfam 01766; Birnavirus VP2 protein
      1. Birnavirus VP2 [141110]
         Link between +sRNA and dsRNA viruses two domains - the first similar to scop_sf 88633 and the second, insert domain is similar to scop_sf 49818. dsRNA virus but unlike the other dsRNA viruses has a genomic arrangement and genomic replication strategy similar to +sRNA viruses
         1. Infectious bursal disease virus [TaxId: 10995] [141111] (41)
            SQ P15480 11-431! SQ P61825 8-440! SQ Q6S9I7 11-429
            1. 2df7
               complexed with ca, cl
               1. region a:11-429 [131449]
            2. 2df7
               automatically matched to 2DF7 A:11-429
               complexed with ca, cl
               1. region b:12-429 [131450]
            3. 2df7
               automatically matched to 2DF7 A:11-429
               complexed with ca, cl
               1. region c:11-428 [131451]
            4. 2df7
               automatically matched to 2DF7 A:11-429
               complexed with ca, cl
               1. region d:11-429 [131452]
            5. 2df7
               automatically matched to 2DF7 A:11-429
               complexed with ca, cl
               1. region e:11-429 [131453]
            6. 2df7
               automatically matched to 2DF7 A:11-429
               complexed with ca, cl
               1. region f:11-427 [131454]
            7. 2df7
               automatically matched to 2DF7 A:11-429
               complexed with ca, cl
               1. region g:12-428 [131455]
            8. 2df7
               automatically matched to 2DF7 A:11-429
               complexed with ca, cl
               1. region h:12-429 [131456]
            9. 2df7
               automatically matched to 2DF7 A:11-429
               complexed with ca, cl
               1. region i:11-428 [131457]
            10. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region j:12-429 [131458]
            11. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region k:12-429 [131459]
            12. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region l:11-428 [131460]
            13. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region m:12-428 [131461]
            14. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region n:11-427 [131462]
            15. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region o:12-429 [131463]
            16. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region p:11-429 [131464]
            17. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region q:11-429 [131465]
            18. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region r:12-427 [131466]
            19. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region s:12-427 [131467]
            20. 2df7
                automatically matched to 2DF7 A:11-429
                complexed with ca, cl
                1. region t:11-428 [131468]
            21. 2gsy
                complexed with ca
                1. region a:8-440 [135599]
            22. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region b:8-440 [135600]
            23. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region c:8-440 [135601]
            24. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region d:8-440 [135602]
            25. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region e:8-440 [135603]
            26. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region f:8-440 [135604]
            27. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region g:8-440 [135605]
            28. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region h:8-440 [135606]
            29. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region i:8-440 [135607]
            30. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region j:8-440 [135608]
            31. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region k:8-440 [135609]
            32. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region l:8-440 [135610]
            33. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region m:8-440 [135611]
            34. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region n:8-440 [135612]
            35. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region o:8-440 [135613]
            36. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region p:8-440 [135614]
            37. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region q:8-440 [135615]
            38. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region r:8-440 [135616]
            39. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region s:8-440 [135617]
            40. 2gsy
                automatically matched to 2GSY A:8-440
                complexed with ca
                1. region t:8-440 [135618]
            41. 1wcd
                1. region j:11-431 [120887]
3. ssDNA viruses [88645] (3)
   uperfamily
   1. Microviridae-like VP [49612] (3)
      1. Microvirus capsid proteins [49613]
         include capsid protein F and spike protein G
         1. Bacteriophage phi-X174 [TaxId: 10847] [49614] (4)
            1. 2bpa
               1. chain 1 [23272]
               2. chain 2 [23273]
            2. 1al0
               1. chain f [23274]
               2. chain g [23275]
            3. 1cd3
               1. chain f [23276]
               2. chain g [23277]
            4. 1kvp
               chimera with a fragment 1-71 of vp1 from spiroplasma virus SPV4
               1. chain a [23278]
         2. Bacteriophage G4 [TaxId: 10843] [49615] (1)
            1. 1gff
               mutant
               1. chain 1 [23279]
               2. chain 2 [23280]
         3. Bacteriophage alpha3 [TaxId: 10849] [82008] (2)
            1. 1m06
               complexed with c
               1. chain f [78326]
               2. chain g [78327]
            2. 1rb8
               complexed with c
               1. chain f [97279]
               2. chain g [97280]
   2. Parvoviridae-like VP [88646] (7)
      1. Parvovirus (panleukopenia virus) capsid protein [49661]
         1. Feline panleukopenia virus, strain b [TaxId: 10786] [49689] (1)
            1. 1fpv
               1. chain a [23579]
         2. Canine parvovirus [TaxId: 10788] [49662] (7)
            1. 1c8d
               complexed with ca
               1. chain a [23375]
            2. 1p5w
               complexed with mg; mutant
               1. chain a [94150]
            3. 2cas
               1. chain a [23376]
            4. 1p5y
               mutant
               1. chain a [94152]
            5. 4dpv
               protein/DNA complex; complexed with mg
               1. chain z [23377]
            6. 1ijs
               protein/DNA complex; mutant
               1. chain p [23379]
            7. 1c8h
               complexed with ca; mutant
               1. chain a [23378]
         3. Feline parvovirus [TaxId: 10785] [49663] (3)
            1. 1c8g
               complexed with ca
               1. chain a [23380]
            2. 1c8f
               complexed with ca
               1. chain a [23381]
            3. 1c8e
               1. chain a [23382]
         4. Porcine parvovirus [TaxId: 10796] [69201] (1)
            1. 1k3v
               1. chain a [68122]
         5. Murine minute virus, strain i [TaxId: 10794] [49665] (2)
            1. 1mvm
               protein/DNA complex
               1. chain a [23383]
            2. 1z1c
               automatically matched to d1mvma_
               complexed with ca, d5m
               1. region a:39-587 [124350]
         6. Human parvovirus B19 [TaxId: 10798] [110116] (1)
            SQ Q9JGS0 246-781
            1. 1s58
               1. chain a [105262]
      2. Dependovirus capsid protein [74887]
         1. Adeno-associated virus, aav-2 [TaxId: 272636] [74888] (1)
            a vector for human genome therapy
            1. 1lp3
               1. chain a [74169]
   3. Densovirinae-like VP [88647] (1)
      1. Densovirus capsid protein [49652]
         1. Galleria mellonella densovirus [TaxId: 37138] [49653] (1)
            1. 1dnv
               1. chain a [23332]
4. Group I dsDNA viruses [88648] (1)
   uperfamily
   1. Papovaviridae-like VP [88649] (3)
      1. Polyomavirus coat proteins [49657]
         1. Murine polyomavirus, strain small-plaque 16 [TaxId: 10634] [49658] (5)
            1. 1vps
               complexed with gal, nag, sia
               1. chain a [23336]
               2. chain b [23337]
               3. chain c [23338]
               4. chain d [23339]
               5. chain e [23340]
            2. 1vpn
               1. chain a [23341]
               2. chain b [23342]
               3. chain c [23343]
               4. chain d [23344]
               5. chain e [23345]
            3. 1cn3
               1. chain a [23346]
               2. chain b [23347]
               3. chain c [23348]
               4. chain d [23349]
               5. chain e [23350]
            4. 1sid
               complexed with gal, glc, sia
               1. chain a [23351]
               2. chain b [23352]
               3. chain c [23353]
               4. chain d [23354]
               5. chain e [23355]
               6. chain f [23356]
            5. 1sie
               complexed with gal, nag, sia
               1. chain a [23357]
               2. chain b [23358]
               3. chain c [23359]
               4. chain d [23360]
               5. chain e [23361]
               6. chain f [23362]
         2. Simian virus 40, Sv40 [TaxId: 10633] [49691] (1)
            1. 1sva
               1. chain 1 [23580]
               2. chain 2 [23581]
               3. chain 3 [23582]
               4. chain 4 [23583]
               5. chain 5 [23584]
               6. chain 6 [23585]
      2. Papillomavirus L1 protein [49692]
         1. Human papillomavirus type 16 [TaxId: 333760] [49693] (1)
            1. 1dzl
               mutant
               1. chain a [23586]
5. Group II dsDNA viruses VP [49749] (3)
   duplication: consists of two domains of this fold packed together like the nucleoplasmin subunits
   trimeric; in the trimers, the domains are arranged around pseudo six-fold axis
   uperfamily
   1. Coat protein p3 [49750] (1)
      1. Coat protein p3 [63403]
         1. Bacteriophage prd1 [TaxId: 10658] [49752] (3)
            1. 1hx6
               complexed with cl, mpd, na
               1. region a:15-244 [58995]
               2. region a:245-384 [58996]
               3. region b:11-244 [58997]
               4. region b:245-384 [58998]
               5. region c:14-244 [58999]
               6. region c:245-384 [59000]
            2. 1cjd
               1. region a:15-244 [58963]
               2. region a:245-383 [58964]
               3. region b:13-244 [58965]
               4. region b:245-384 [58966]
               5. region c:16-244 [58967]
               6. region c:247-384 [58968]
            3. 1hqn
               1. region a:16-244 [58989]
               2. region a:245-384 [58990]
               3. region b:15-244 [58991]
               4. region b:245-384 [58992]
               5. region c:14-244 [58993]
               6. region c:245-385 [58994]
   2. Major capsid protein vp54 [82013] (1)
      1. Major capsid protein vp54 [82014]
         1. Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506] [82015] (2)
            a large, lipid-containing, DNA virus
            1. 1m3y
               complexed with hg, man, nag
               1. region a:25-221 [78579]
               2. region a:222-437 [78580]
               3. region b:25-221 [78581]
               4. region b:222-437 [78582]
               5. region c:25-221 [78583]
               6. region c:222-437 [78584]
               7. region d:25-221 [78585]
               8. region d:222-437 [78586]
            2. 1j5q
               complexed with hg, man, nag
               1. region a:25-221 [77084]
               2. region a:222-437 [77085]
               3. region b:25-221 [77086]
               4. region b:222-437 [77087]
   3. Adenovirus hexon [49753] (2)
      each domain is heavily decorated with many insertions
      1. Adenovirus hexon [63404]
         1. Human adenovirus type 2 [TaxId: 10515] [49755] (1)
            1. 1p2z
               complexed with cit
               1. region a:5-650 [93962]
               2. region a:651-962 [93963]
         2. Human adenovirus type 5 [TaxId: 28285] [49756] (25)
            1. 1p30
               1. region a:5-636 [93964]
               2. region a:637-946 [93965]
            2. 2bvi
               automatically matched to d1p30a1
               1. region f:5-636 [129258]
            3. 2bvi
               automatically matched to d1p30a2
               1. region f:637-946 [129259]
            4. 2bvi
               automatically matched to d1p30a1
               1. region g:5-636 [129260]
            5. 2bvi
               automatically matched to d1p30a2
               1. region g:637-946 [129261]
            6. 2bvi
               automatically matched to d1p30a1
               1. region h:5-636 [129262]
            7. 2bvi
               automatically matched to d1p30a2
               1. region h:637-946 [129263]
            8. 2bvi
               automatically matched to d1p30a1
               1. region i:5-636 [129264]
            9. 2bvi
               automatically matched to d1p30a2
               1. region i:637-946 [129265]
            10. 2bvi
                automatically matched to d1p30a1
                1. region j:5-636 [129266]
            11. 2bvi
                automatically matched to d1p30a2
                1. region j:637-946 [129267]
            12. 2bvi
                automatically matched to d1p30a1
                1. region k:5-636 [129268]
            13. 2bvi
                automatically matched to d1p30a2
                1. region k:637-946 [129269]
            14. 2bvi
                automatically matched to d1p30a1
                1. region l:5-636 [129270]
            15. 2bvi
                automatically matched to d1p30a2
                1. region l:637-946 [129271]
            16. 2bvi
                automatically matched to d1p30a1
                1. region m:5-636 [129272]
            17. 2bvi
                automatically matched to d1p30a2
                1. region m:637-946 [129273]
            18. 2bvi
                automatically matched to d1p30a1
                1. region n:5-636 [129274]
            19. 2bvi
                automatically matched to d1p30a2
                1. region n:637-946 [129275]
            20. 2bvi
                automatically matched to d1p30a1
                1. region o:5-636 [129276]
            21. 2bvi
                automatically matched to d1p30a2
                1. region o:637-946 [129277]
            22. 2bvi
                automatically matched to d1p30a1
                1. region p:5-636 [129278]
            23. 2bvi
                automatically matched to d1p30a2
                1. region p:637-946 [129279]
            24. 2bvi
                automatically matched to d1p30a1
                1. region q:5-636 [129280]
            25. 2bvi
                automatically matched to d1p30a2
                1. region q:637-946 [129281]
6. Satellite viruses [88650] (1)
   uperfamily
   1. Satellite viruses [88651] (3)
      1. SPMV coat protein [49617]
         1. Satellite panicum mosaic virus [TaxId: 154834] [49618] (1)
            1. 1stm
               1. chain a [23281]
               2. chain b [23282]
               3. chain c [23283]
               4. chain d [23284]
               5. chain e [23285]
      2. STMV coat protein [49619]
         1. Satellite tobacco mosaic virus [TaxId: 12881] [49620] (1)
            1. 1a34
               protein/RNA complex; complexed with so4
               1. chain a [23286]
      3. STNV coat protein [49621]
         1. Satellite tobacco necrosis virus [TaxId: 12881] [49622] (1)
            1. 2buk
               automatically matched to d2stv__
               complexed with ca
               1. region a:12-195 [129220]
7. PHM/PNGase F [49742] (2)
   members of this superfamily bind peptide substrates
   duplication: consists of two domains of this fold packed together like the adjacent nucleoplasmin subunits
   uperfamily
   1. Glycosyl-asparaginase [49743] (1)
      1. Peptide:N-glycosidase F, PNGase F [49744]
         1. Flavobacterium meningosepticum [TaxId: 238] [49745] (3)
            1. 1pgs
               1. region a:4-140 [23653]
               2. region a:141-314 [23654]
            2. 1pnf
               complexed with nag, so4
               1. region a:1-140 [23655]
               2. region a:141-314 [23656]
            3. 1png
               1. region a:5-140 [23657]
               2. region a:141-314 [23658]
   2. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [49746] (1)
      1. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [63402]
         1. Rat (Rattus norvegicus) [TaxId: 10116] [49748] (12)
            1. 1yi9
               automatically matched to d1opma1
               complexed with cu, gol; mutant
               1. region a:47-198 [123276]
            2. 1yi9
               automatically matched to d1sdwa2
               complexed with cu, gol; mutant
               1. region a:199-355 [123277]
            3. 1sdw
               complexed with cu, gol, iyt, ni, o2
               1. region a:45-198 [98810]
               2. region a:199-356 [98811]
            4. 1phm
               complexed with azi, cu, gol
               1. region a:45-198 [59015]
               2. region a:199-354 [59016]
            5. 1yjk
               automatically matched to d1opma1
               complexed with cu, gol
               1. region a:50-198 [123423]
            6. 1yjk
               automatically matched to d1sdwa2
               complexed with cu, gol
               1. region a:199-355 [123424]
            7. 3phm
               complexed with 1cu, azi, cu, gol, ni1
               1. region a:45-198 [59060]
               2. region a:199-354 [59061]
            8. 1opm
               complexed with 1cu, azi, cu, gol, iyg, ni1
               1. region a:45-198 [59013]
               2. region a:199-354 [59014]
            9. 1yip
               automatically matched to d1opma1
               complexed with cu
               1. region a:45-198 [123328]
            10. 1yip
                automatically matched to d1sdwa2
                complexed with cu
                1. region a:199-355 [123329]
            11. 1yjl
                automatically matched to d1opma1
                mutant
                1. region a:50-198 [123425]
            12. 1yjl
                automatically matched to d1sdwa2
                mutant
                1. region a:199-355 [123426]

Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009 Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk