Structural Classification of Proteins

Fold: Sm-like fold

: core: barrel, open; n*=4, S*=8; meander; SH3-like topology

Lineage:

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

Superfamilies:

Sm-like ribonucleoproteins [50182] (6)
uperfamily
1. 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)
  2. D2 core SNRNP protein [50186]
    1. Human (Homo sapiens) [TaxId: 9606] [50187] (1)
  3. D3 core SNRNP protein [50188]
    1. Human (Homo sapiens) [TaxId: 9606] [50189] (1)
  4. B core SNRNP protein [50190]
    1. Human (Homo sapiens) [TaxId: 9606] [50191] (1)
  5. Small nuclear ribonucleoprotein F, Smf [82087]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82088] (2)
  6. Archaeal homoheptameric Sm protein [63758]
    1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63759] (5)
      MTH649, smap1
    2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [63760] (2)
      smap1
    3. Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234] [63761] (2)
    4. Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234] [74938] (1)
    5. Archaeon Pyrococcus abyssi [TaxId: 29292] [82089] (2)
    6. Sulfolobus solfataricus [TaxId: 2287] [141290] (14)
      SQ Q97ZQ0 1-76
      SnRNP-2
  7. Sm-Like archaeal protein Smap3 [89317]
    contains additional C-terminal alpha+beta domain
    1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [89318] (1)
  8. U6 snRNA-associated sm-like protein LSM5 [141291]
    1. Cryptosporidium parvum [TaxId: 5807] [141292] (2)
      SQ Q5CXX3 24-115
2. Pleiotropic translational regulator Hfq [74939] (3)
  forms homohexameric ring structures
  1. Pleiotropic translational regulator Hfq [74940]
    1. Staphylococcus aureus [TaxId: 1280] [74941] (2)
    2. Escherichia coli [TaxId: 562] [89319] (1)
    3. Pseudomonas aeruginosa [TaxId: 287] [141293] (12)
      SQ Q9HUM0 6-71
3. 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)
4. 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
5. 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
6. 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
  2. Uncharacterized protein YgdI [159055]
    1. Salmonella typhimurium [TaxId: 90371] [159056] (6)
      SQ Q7CPV8 23-75
  3. Uncharacterized protein ECA1013 [159057]
    1. Erwinia carotovora [TaxId: 554] [159058] (7)
      SQ Q6D8G1 21-73
  4. Putative outer membrane lipoprotein STM1585 [159059]
    1. Salmonella typhimurium [TaxId: 90371] [159060] (3)
      SQ Q7CQI7 22-73
  5. Uncharacterized protein PSPPH2109 [159061]
    1. Pseudomonas syringae [TaxId: 317] [159062] (1)
      SQ Q48JU9 23-74
  6. Hypothetical lipoprotein YgdR [159063]
    1. Escherichia coli [TaxId: 562] [159064] (1)
      SQ P65294 23-72
YhbC-like, C-terminal domain [74942] (1)
uperfamily
1. YhbC-like, C-terminal domain [74943] (1)
  1. Hypothetical protein SP14.3 (SP0552) [74944]
    1. Streptococcus pneumoniae [TaxId: 1313] [74945] (1)
GatD N-terminal domain-like [141300] (1)
uperfamily
1. GatD N-terminal domain-like [141301] (2)
  PfamB 010580
  1. Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD [141302]
    1. Pyrococcus abyssi [TaxId: 29292] [141303] (2)
      SQ Q9V0T9 2-75
    2. Methanobacterium thermoautotrophicum [TaxId: 145262] [141304] (2)
      SQ O26802 2-73
Dom34/Pelota N-terminal domain-like [159065] (1)
1. Dom34/Pelota N-terminal domain-like [159066] (2)
  Warning: Pfam incorrectly assigns this domain to the same family as the structurally unrelated N-terminal domain of eRF1 (Pfam 03463)
  1. Cell division protein pelota [159067]
    1. Thermoplasma acidophilum [TaxId: 2303] [159068] (1)
      SQ Q9HJ74 1-126
  2. Dom34 [159069]
    1. Saccharomyces cerevisiae [TaxId: 4932] [159070] (3)
      SQ P33309 1-135
TrmB C-terminal domain-like [159071] (1)
sugar-binding domain; permuted OB-fold?
1. TrmB C-terminal domain-like [159072] (1)
  C-terminal part of PfamB 004822
  1. Transcriptional regulator TrmB [159073]
    1. Thermococcus litoralis [TaxId: 2265] [159074] (1)
      SQ Q7LYW4 247-338