Structural Classification of Proteins

Superfamily: Positive stranded ssRNA viruses

: uperfamily

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
Superfamily: Positive stranded ssRNA viruses [88633]
uperfamily

Families:

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)
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)
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)
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)
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)
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)
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
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)
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