Structural Classification of Proteins

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:

Root: scop
Class: All beta proteins [48724]
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:

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)
  2. Chromatin decondensation protein 1 (Crp1, Nlp) [89223]
    1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89224] (1)
  3. Nucleophosmin (NO38) [117086]
    1. African clawed frog (Xenopus laevis) [TaxId: 8355] [117087] (2)
      SQ P07222 16-122
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)
    2. Human coxsackievirus A9 [TaxId: 12067] [49683] (1)
    3. Human echovirus 1 [TaxId: 46633] [49685] (1)
    4. Human echovirus 11 [TaxId: 12078] [74890] (4)
  2. Bovine enterovirus coat proteins [49676]
    1. Bovine enterovirus, VG-5-27 [TaxId: 12064] [49677] (1)
  3. Poliovirus coat proteins [49666]
    1. Poliovirus type 1, strain Mahoney [TaxId: 12080] [49667] (12)
    2. Poliovirus type 2, strain Lansing [TaxId: 12083] [49668] (1)
    3. Poliovirus type 3, strain Sabin [TaxId: 12086] [49669] (7)
  4. Rhinovirus coat proteins [49670]
    1. Human rhinovirus B 14 (HRV-14) [TaxId: 12131] [49671] (30)
    2. Human rhinovirus 16, (HRV-16) [TaxId: 31708] [49672] (9)
    3. Human rhinovirus A 1A (HRV-1A) [TaxId: 12134] [49673] (4)
    4. Human rhinovirus A 2 (HRV-2) [TaxId: 12130] [49674] (2)
    5. Human rhinovirus 3, (HRV-3) [TaxId: 44130] [49675] (1)
  5. Aphthovirus (Foot-and-mouth disease virus) coat proteins [49659]
    1. FMDV (Foot-and-mouth disease virus), strain bfs, 1860 [TaxId: 12110] [49660] (4)
  6. Theilovirus capsid proteins [49686]
    1. Theiler's murine encephalomyelitis virus, strain da [TaxId: 12124] [49687] (2)
  7. Mengo encephalomyocarditis virus coat proteins [49678]
    1. Mengovirus [TaxId: 12107] [49679] (2)
  8. Swine vesicular disease virus coat proteins [89225]
    1. Swine vesicular disease virus [TaxId: 12075] [89226] (2)
  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)
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)
  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)
    2. BPMV (Bean pod mottle virus) [TaxId: 12260] [49628] (3)
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)
4. Nodaviridae-like VP [88638] (3)
  1. Alphanodavirus capsid protein [49648]
    1. Black beetle virus [TaxId: 12285] [49649] (1)
    2. Nodamura virus [TaxId: 12288] [49650] (1)
    3. Pariacoto virus [TaxId: 103782] [49651] (1)
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)
6. Bromoviridae-like VP [88639] (4)
  1. Cucumovirus coat protein [88640]
    1. CMV (Cucumber mosaic virus), strain fny [TaxId: 12305] [49646] (1)
    2. TAV (Tomato aspermy virus) [TaxId: 12315] [82012] (1)
    3. BMV (Brome mosaic virus) [TaxId: 12302] [74886] (31)
    4. Cowpea chlorotic mottle virus [TaxId: 12303] [49636] (1)
7. Tymoviridae-like VP [88641] (3)
  1. Tymovirus coat protein [88642]
    1. PHMV (Physalis mottle virus) [TaxId: 72539] [49642] (2)
    2. DYMV (Desmodium yellow mottle tymovirus) [TaxId: 70821] [49644] (1)
    3. TYMV (Turnip yellow mosaic virus) [TaxId: 12154] [49640] (2)
      SQ P03608
8. Tombusviridae-like VP [88643] (7)
  1. Necrovirus coat protein [49637]
    1. TNV (Tobacco necrosis virus) [TaxId: 12054] [49638] (1)
  2. Tombusvirus coat protein [49633]
    1. TBSV (Tomato bushy stunt virus) [TaxId: 12145] [49634] (1)
  3. Carmovirus coat protein [89228]
    1. CarMV (Carnation mottle virus) [TaxId: 11986] [89229] (1)
  4. Sobemovirus coat protein [88644]
    1. SMV (Sesbania mosaic virus) [TaxId: 12558] [49624] (7)
      SQ Q9EB06
    2. SBMV (Southern bean mosaic virus), cow pea strain [TaxId: 12139] [49632] (1)
    3. RYMV (Rice yellow mottle virus) [TaxId: 31744] [49626] (1)
    4. Cocksfoot mottle virus [TaxId: 40979] [82010] (1)
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
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)
    2. Bacteriophage G4 [TaxId: 10843] [49615] (1)
    3. Bacteriophage alpha3 [TaxId: 10849] [82008] (2)
2. Parvoviridae-like VP [88646] (7)
  1. Parvovirus (panleukopenia virus) capsid protein [49661]
    1. Feline panleukopenia virus, strain b [TaxId: 10786] [49689] (1)
    2. Canine parvovirus [TaxId: 10788] [49662] (7)
    3. Feline parvovirus [TaxId: 10785] [49663] (3)
    4. Porcine parvovirus [TaxId: 10796] [69201] (1)
    5. Murine minute virus, strain i [TaxId: 10794] [49665] (2)
    6. Human parvovirus B19 [TaxId: 10798] [110116] (1)
      SQ Q9JGS0 246-781
  2. Dependovirus capsid protein [74887]
    1. Adeno-associated virus, aav-2 [TaxId: 272636] [74888] (1)
      a vector for human genome therapy
3. Densovirinae-like VP [88647] (1)
  1. Densovirus capsid protein [49652]
    1. Galleria mellonella densovirus [TaxId: 37138] [49653] (1)
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)
    2. Simian virus 40, Sv40 [TaxId: 10633] [49691] (1)
  2. Papillomavirus L1 protein [49692]
    1. Human papillomavirus type 16 [TaxId: 333760] [49693] (1)
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)
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
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)
    2. Human adenovirus type 5 [TaxId: 28285] [49756] (25)
Satellite viruses [88650] (1)
uperfamily
1. Satellite viruses [88651] (3)
  1. SPMV coat protein [49617]
    1. Satellite panicum mosaic virus [TaxId: 154834] [49618] (1)
  2. STMV coat protein [49619]
    1. Satellite tobacco mosaic virus [TaxId: 12881] [49620] (1)
  3. STNV coat protein [49621]
    1. Satellite tobacco necrosis virus [TaxId: 12881] [49622] (1)
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)
2. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [49746] (1)
  1. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [63402]
    1. Rat (Rattus norvegicus) [TaxId: 10116] [49748] (12)