Structural Classification of Proteins

Superfamily: Sm-like ribonucleoproteins

: uperfamily

Lineage:

Root: scop
Class: All beta proteins [48724]
Fold: Sm-like fold [50181]
core: barrel, open; n*=4, S*=8; meander; SH3-like topology
Superfamily: Sm-like ribonucleoproteins [50182]
uperfamily

Families:

Sm motif of small nuclear ribonucleoproteins, SNRNP [50183] (13)
forms homo and heteroheptameric ring structures
1. D1 core SNRNP protein [50184]
  1. Human (Homo sapiens) [TaxId: 9606] [50185] (1)
    1. 1b34
      1. chain a [24796]
2. D2 core SNRNP protein [50186]
  1. Human (Homo sapiens) [TaxId: 9606] [50187] (1)
    1. 1b34
      1. chain b [24797]
3. D3 core SNRNP protein [50188]
  1. Human (Homo sapiens) [TaxId: 9606] [50189] (1)
    1. 1d3b
      CASP3
      1. chain a [24798]
      2. chain c [24799]
      3. chain e [24800]
      4. chain g [24801]
      5. chain i [24802]
      6. chain k [24803]
4. B core SNRNP protein [50190]
  1. Human (Homo sapiens) [TaxId: 9606] [50191] (1)
    1. 1d3b
      CASP3
      1. chain b [24804]
      2. chain d [24805]
      3. chain f [24806]
      4. chain h [24807]
      5. chain j [24808]
      6. chain l [24809]
5. Small nuclear ribonucleoprotein F, Smf [82087]
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82088] (2)
    1. 1n9r
      1. chain a [80344]
      2. chain b [80345]
      3. chain c [80346]
      4. chain d [80347]
      5. chain e [80348]
      6. chain f [80349]
      7. chain g [80350]
    2. 1n9s
      1. chain a [80351]
      2. chain b [80352]
      3. chain c [80353]
      4. chain d [80354]
      5. chain e [80355]
      6. chain f [80356]
      7. chain g [80357]
      8. chain h [80358]
      9. chain i [80359]
      10. chain j [80360]
      11. chain k [80361]
      12. chain l [80362]
      13. chain m [80363]
      14. chain n [80364]
6. Archaeal homoheptameric Sm protein [63758]
  1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63759] (5)
    MTH649, smap1
    1. 1mgq
      1. chain a [79099]
      2. chain b [79100]
      3. chain c [79101]
      4. chain d [79102]
      5. chain e [79103]
      6. chain f [79104]
      7. chain g [79105]
    2. 1jbm
      structural genomics
      complexed with acy, edo
      1. chain a [84143]
      2. chain b [84144]
      3. chain c [84145]
      4. chain d [84146]
      5. chain e [84147]
      6. chain f [84148]
      7. chain g [84149]
    3. 1i81
      1. chain a [61930]
      2. chain b [61931]
      3. chain c [61932]
      4. chain d [61933]
      5. chain e [61934]
      6. chain f [61935]
      7. chain g [61936]
    4. 1loj
      complexed with mpd, u, uri
      1. chain a [84650]
      2. chain b [84651]
      3. chain c [84652]
      4. chain d [84653]
      5. chain e [84654]
      6. chain f [84655]
      7. chain g [84656]
      8. chain h [84657]
      9. chain i [84658]
      10. chain j [84659]
      11. chain k [84660]
      12. chain l [84661]
      13. chain m [84662]
      14. chain n [84663]
    5. 1jri
      complexed with cl, edo
      1. chain a [67121]
      2. chain b [67122]
      3. chain c [67123]
      4. chain d [67124]
      5. chain e [67125]
      6. chain f [67126]
      7. chain g [67127]
      8. chain h [67128]
      9. chain i [67129]
      10. chain j [67130]
      11. chain k [67131]
      12. chain l [67132]
      13. chain m [67133]
      14. chain n [67134]
  2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [63760] (2)
    smap1
    1. 1i8f
      complexed with gol
      1. chain a [61959]
      2. chain b [61960]
      3. chain c [61961]
      4. chain d [61962]
      5. chain e [61963]
      6. chain f [61964]
      7. chain g [61965]
    2. 1lnx
      complexed with acy, gol, uri
      1. chain a [84642]
      2. chain b [84643]
      3. chain c [84644]
      4. chain d [84645]
      5. chain e [84646]
      6. chain f [84647]
      7. chain g [84648]
  3. Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234] [63761] (2)
    1. 1i4k
      complexed with cit
      1. chain a [61692]
      2. chain b [61693]
      3. chain c [61694]
      4. chain d [61695]
      5. chain e [61696]
      6. chain f [61697]
      7. chain g [61698]
      8. chain h [61699]
      9. chain i [61700]
      10. chain j [61701]
      11. chain k [61702]
      12. chain l [61703]
      13. chain m [61704]
      14. chain n [61705]
      15. chain o [61706]
      16. chain p [61707]
      17. chain q [61708]
      18. chain r [61709]
      19. chain s [61710]
      20. chain t [61711]
      21. chain u [61712]
      22. chain v [61713]
      23. chain w [61714]
      24. chain x [61715]
      25. chain y [61716]
      26. chain z [61717]
      27. chain 1 [61690]
      28. chain 2 [61691]
    2. 1i5l
      complexed with short poly-U RNA
      complexed with uri
      1. chain a [61791]
      2. chain b [61792]
      3. chain c [61793]
      4. chain d [61794]
      5. chain e [61795]
      6. chain f [61796]
      7. chain g [61797]
      8. chain h [61798]
      9. chain i [61799]
      10. chain j [61800]
      11. chain k [61801]
      12. chain l [61802]
      13. chain m [61803]
      14. chain n [61804]
  4. Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234] [74938] (1)
    1. 1ljo
      complexed with acy, cd; mutant
      1. chain a [73941]
  5. Archaeon Pyrococcus abyssi [TaxId: 29292] [82089] (2)
    1. 1h64
      1. chain a [76677]
      2. chain b [76678]
      3. chain c [76679]
      4. chain d [76680]
      5. chain e [76681]
      6. chain f [76682]
      7. chain g [76683]
      8. chain h [76684]
      9. chain i [76685]
      10. chain j [76686]
      11. chain k [76687]
      12. chain l [76688]
      13. chain m [76689]
      14. chain n [76690]
      15. chain o [76691]
      16. chain p [76692]
      17. chain q [76693]
      18. chain r [76694]
      19. chain s [76695]
      20. chain t [76696]
      21. chain u [76697]
      22. chain v [76698]
      23. chain w [76699]
      24. chain x [76700]
      25. chain y [76701]
      26. chain z [76702]
      27. chain 1 [76675]
      28. chain 2 [76676]
    2. 1m8v
      complexed with a uridine heptamer
      complexed with ca, u
      1. chain a [78814]
      2. chain b [78815]
      3. chain c [78816]
      4. chain d [78817]
      5. chain e [78818]
      6. chain f [78819]
      7. chain g [78820]
      8. chain h [78821]
      9. chain i [78822]
      10. chain j [78823]
      11. chain k [78824]
      12. chain l [78825]
      13. chain m [78826]
      14. chain n [78827]
  6. Sulfolobus solfataricus [TaxId: 2287] [141290] (14)
    SQ Q97ZQ0 1-76
    SnRNP-2
    1. 1th7
      1. region a:3-78 [119264]
    2. 1th7
      automatically matched to 1TH7 A:3-78
      1. region b:3-78 [119265]
    3. 1th7
      automatically matched to 1TH7 A:3-78
      1. region c:3-78 [119266]
    4. 1th7
      automatically matched to 1TH7 A:3-78
      1. region d:3-78 [119267]
    5. 1th7
      automatically matched to 1TH7 A:3-78
      1. region e:3-78 [119268]
    6. 1th7
      automatically matched to 1TH7 A:3-78
      1. region f:3-78 [119269]
    7. 1th7
      automatically matched to 1TH7 A:3-78
      1. region g:3-78 [119270]
    8. 1th7
      automatically matched to 1TH7 A:3-78
      1. region h:3-78 [119271]
    9. 1th7
      automatically matched to 1TH7 A:3-78
      1. region i:3-78 [119272]
    10. 1th7
      automatically matched to 1TH7 A:3-78
      1. region j:3-78 [119273]
    11. 1th7
      automatically matched to 1TH7 A:3-78
      1. region k:3-78 [119274]
    12. 1th7
      automatically matched to 1TH7 A:3-78
      1. region l:3-78 [119275]
    13. 1th7
      automatically matched to 1TH7 A:3-78
      1. region m:3-78 [119276]
    14. 1th7
      automatically matched to 1TH7 A:3-78
      1. region n:3-78 [119277]
7. Sm-Like archaeal protein Smap3 [89317]
  contains additional C-terminal alpha+beta domain
  1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [89318] (1)
    1. 1m5q
      complexed with acy, cd, gol, mse, na
      1. chain a [84810]
      2. chain b [84811]
      3. chain c [84812]
      4. chain d [84813]
      5. chain e [84814]
      6. chain f [84815]
      7. chain g [84816]
      8. chain h [84817]
      9. chain i [84818]
      10. chain j [84819]
      11. chain k [84820]
      12. chain l [84821]
      13. chain m [84822]
      14. chain n [84823]
      15. chain o [84824]
      16. chain p [84825]
      17. chain q [84826]
      18. chain r [84827]
      19. chain s [84828]
      20. chain t [84829]
      21. chain u [84830]
      22. chain v [84831]
      23. chain w [84832]
      24. chain x [84833]
      25. chain y [84834]
      26. chain z [84835]
      27. chain 1 [84808]
      28. chain 2 [84809]
8. U6 snRNA-associated sm-like protein LSM5 [141291]
  1. Cryptosporidium parvum [TaxId: 5807] [141292] (2)
    SQ Q5CXX3 24-115
    1. 2fwk
      1. region a:24-115 [134245]
    2. 2fwk
      automatically matched to 2FWK A:24-115
      1. region b:26-113 [134246]
Pleiotropic translational regulator Hfq [74939] (3)
forms homohexameric ring structures
1. Pleiotropic translational regulator Hfq [74940]
  1. Staphylococcus aureus [TaxId: 1280] [74941] (2)
    1. 1kq1
      complexed with acy
      1. chain a [72848]
      2. chain b [72849]
      3. chain h [72850]
      4. chain i [72851]
      5. chain k [72852]
      6. chain m [72853]
      7. chain s [72856]
      8. chain t [72857]
      9. chain y [72859]
      10. chain n [72854]
      11. chain r [72855]
      12. chain w [72858]
    2. 1kq2
      1. chain a [72860]
      2. chain b [72861]
      3. chain h [72862]
      4. chain i [72863]
      5. chain k [72864]
      6. chain m [72865]
  2. Escherichia coli [TaxId: 562] [89319] (1)
    1. 1hk9
      1. chain a [83541]
      2. chain b [83542]
      3. chain c [83543]
      4. chain d [83544]
      5. chain e [83545]
      6. chain f [83546]
  3. Pseudomonas aeruginosa [TaxId: 287] [141293] (12)
    SQ Q9HUM0 6-71
    1. 1u1s
      1. region a:6-71 [119451]
    2. 1u1s
      automatically matched to 1U1S A:6-71
      1. region b:6-70 [119452]
    3. 1u1s
      automatically matched to 1U1S A:6-71
      1. region c:6-69 [119453]
    4. 1u1s
      automatically matched to 1U1S A:6-71
      1. region d:6-71 [119454]
    5. 1u1s
      automatically matched to 1U1S A:6-71
      1. region e:6-69 [119455]
    6. 1u1s
      automatically matched to 1U1S A:6-71
      1. region f:6-69 [119456]
    7. 1u1t
      automatically matched to 1U1S A:6-71
      1. region a:6-71 [119457]
    8. 1u1t
      automatically matched to 1U1S A:6-71
      1. region b:6-70 [119458]
    9. 1u1t
      automatically matched to 1U1S A:6-71
      1. region c:6-69 [119459]
    10. 1u1t
      automatically matched to 1U1S A:6-71
      1. region d:6-71 [119460]
    11. 1u1t
      automatically matched to 1U1S A:6-71
      1. region e:6-71 [119461]
    12. 1u1t
      automatically matched to 1U1S A:6-71
      1. region f:6-70 [119462]
Mechanosensitive channel protein MscS (YggB), middle domain [82090] (1)
1. Mechanosensitive channel protein MscS (YggB), middle domain [82091]
  forms homoheptameric ring structure very similar to those of the archaeal and eukaryotic Sm proteins
  1. Escherichia coli [TaxId: 562] [82092] (14)
    1. 2vv5
      automatically matched to d2oaua1
      mutant
      1. region a:113-179 [153613]
    2. 2vv5
      automatically matched to d2oaua1
      mutant
      1. region b:113-179 [153616]
    3. 2vv5
      automatically matched to d2oaua1
      mutant
      1. region c:113-179 [153619]
    4. 2vv5
      automatically matched to d2oaua1
      mutant
      1. region d:113-179 [153622]
    5. 2vv5
      automatically matched to d2oaua1
      mutant
      1. region e:113-179 [153625]
    6. 2vv5
      automatically matched to d2oaua1
      mutant
      1. region f:113-179 [153628]
    7. 2vv5
      automatically matched to d2oaua1
      mutant
      1. region g:113-179 [153631]
    8. 2oau
      automatically matched to d1mxma1
      1. region a:113-179 [138978]
    9. 2oau
      automatically matched to d1mxma1
      1. region b:113-179 [138981]
    10. 2oau
      automatically matched to d1mxma1
      1. region c:113-179 [138984]
    11. 2oau
      automatically matched to d1mxma1
      1. region d:113-179 [138987]
    12. 2oau
      automatically matched to d1mxma1
      1. region e:113-179 [138990]
    13. 2oau
      automatically matched to d1mxma1
      1. region f:113-179 [138993]
    14. 2oau
      automatically matched to d1mxma1
      1. region g:113-179 [138996]
PF1955-like [141294] (1)
homohexadecameric assembly: two stacked octameric rings
1. Hypothetical protein PF1955 [141295]
  1. Pyrococcus furiosus [TaxId: 2261] [141296] (4)
    SQ Q8TZN2 5-70
    1. 1ycy
      1. region a:5-70 [122970]
    2. 1ycy
      automatically matched to 1YCY A:5-70
      1. region b:5-70 [122971]
    3. 1ycy
      automatically matched to 1YCY A:5-70
      1. region c:5-70 [122972]
    4. 1ycy
      automatically matched to 1YCY A:5-70
      1. region d:5-70 [122973]
LSM14 N-terminal domain-like [141297] (1)
1. LSM14 homolog A (Lsm14a) [141298]
  1. Zebrafish (Danio rerio) [TaxId: 7955] [141299] (2)
    SQ Q6P111 6-85
    1. 2vxf
      automatically matched to d2fb7a1
      mutant
      1. region a:6-85 [153679]
    2. 2fb7
      1. region a:16-95 [133238]
YgdI/YgdR-like [159052] (6)
Pfam 06004; DUF903, putative lipoprotein; both homohexameric and homoheptameric ring assemblies are observed in the crystals
1. Uncharacterized protein SO0963 [159053]
  1. Shewanella oneidensis [TaxId: 70863] [159054] (2)
    SQ Q8EI81 25-76
    1. 2rb6
      1. region a:25-76 [151844]
    2. 2rb6
      automatically matched to 2RB6 A:25-76
      1. region b:25-76 [151845]
2. Uncharacterized protein YgdI [159055]
  1. Salmonella typhimurium [TaxId: 90371] [159056] (6)
    SQ Q7CPV8 23-75
    1. 2ra2
      1. region a:4-56 [151811]
    2. 2ra2
      automatically matched to 2RA2 A:4-56
      1. region b:4-56 [151812]
    3. 2ra2
      automatically matched to 2RA2 A:4-56
      1. region c:4-56 [151813]
    4. 2ra2
      automatically matched to 2RA2 A:4-56
      1. region d:4-56 [151814]
    5. 2ra2
      automatically matched to 2RA2 A:4-56
      1. region e:4-56 [151815]
    6. 2ra2
      automatically matched to 2RA2 A:4-56
      1. region f:4-55 [151816]
3. Uncharacterized protein ECA1013 [159057]
  1. Erwinia carotovora [TaxId: 554] [159058] (7)
    SQ Q6D8G1 21-73
    1. 3bdu
      1. region a:2-54 [155154]
    2. 3bdu
      automatically matched to 3BDU A:2-54
      1. region b:2-53 [155155]
    3. 3bdu
      automatically matched to 3BDU A:2-54
      1. region c:2-53 [155156]
    4. 3bdu
      automatically matched to 3BDU A:2-54
      1. region d:2-53 [155157]
    5. 3bdu
      automatically matched to 3BDU A:2-54
      1. region e:2-54 [155158]
    6. 3bdu
      automatically matched to 3BDU A:2-54
      1. region f:2-53 [155159]
    7. 3bdu
      automatically matched to 3BDU A:2-54
      1. region g:2-53 [155160]
4. Putative outer membrane lipoprotein STM1585 [159059]
  1. Salmonella typhimurium [TaxId: 90371] [159060] (3)
    SQ Q7CQI7 22-73
    1. 2rd1
      1. region a:22-73 [151915]
    2. 2rd1
      automatically matched to 2RD1 A:22-73
      1. region b:22-73 [151916]
    3. 2rd1
      automatically matched to 2RD1 A:22-73
      1. region c:22-73 [151917]
5. Uncharacterized protein PSPPH2109 [159061]
  1. Pseudomonas syringae [TaxId: 317] [159062] (1)
    SQ Q48JU9 23-74
    1. 2k57
      1. region a:2-53 [148272]
6. Hypothetical lipoprotein YgdR [159063]
  1. Escherichia coli [TaxId: 562] [159064] (1)
    SQ P65294 23-72
    1. 2jn0
      1. region a:4-53 [148141]