SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

Lineage for Protein: automated matches

  1. Root: SCOPe 2.06
  2. 2017114Class b: All beta proteins [48724] (177 folds)
  3. 2075417Fold b.121: Nucleoplasmin-like/VP (viral coat and capsid proteins) [88632] (7 superfamilies)
    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
  4. 2075626Superfamily b.121.4: Positive stranded ssRNA viruses [88633] (10 families) (S)
  5. 2075627Family b.121.4.1: Picornaviridae-like VP (VP1, VP2, VP3 and VP4) [88634] (10 protein domains)
    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)
  6. 2075905Protein automated matches [190854] (13 species)
    not a true protein

Species:

  1. 2075906Coxsackievirus a16 (strain tainan/5079/98) [TaxId:231417] [277504] (1 PDB entry)
  2. 2075908Coxsackievirus a16 [TaxId:31704] [276274] (3 PDB entries)
    1. Domain for 5abj:
    2. Domain for 5c4w:
    3. Domain for 5c9a:
  3. 2075912Coxsackievirus a24 [TaxId:12089] [260750] (4 PDB entries)
    1. Domains for 4q4v:
      1. 2075919Domain d4q4v1_: 4q4v 1: [267264]
        automated match to d2plv1_
      2. 2075920Domain d4q4v3_: 4q4v 3: [267265]
        automated match to d4q4y3_
    2. Domains for 4q4w:
      1. 2075913Domain d4q4w1_: 4q4w 1: [267266]
        automated match to d2plv1_
        complexed with ca, cl, hez
      2. 2075914Domain d4q4w3_: 4q4w 3: [267267]
        automated match to d4q4y3_
        complexed with ca, cl, hez
    3. Domains for 4q4x:
      1. 2075915Domain d4q4x1_: 4q4x 1: [260751]
        automated match to d2plv1_
        complexed with ca, cl, hez, na, sia
      2. 2075916Domain d4q4x3_: 4q4x 3: [263630]
        automated match to d4q4y3_
        complexed with ca, cl, hez, na, sia
    4. Domains for 4q4y:
      1. 2075917Domain d4q4y1_: 4q4y 1: [263631]
        automated match to d2plv1_
        complexed with ca, cl, hez, mg, myr, sia
      2. 2075918Domain d4q4y3_: 4q4y 3: [260752]
        automated match to d1hxs3_
        complexed with ca, cl, hez, mg, myr, sia
  4. 2075921Foot-and-mouth disease virus - type a [TaxId:12111] [196861] (4 PDB entries)
    1. Domains for 4gh4:
      1. 2075924Domain d4gh4a_: 4gh4 A: [252214]
        automated match to d4iv1a_
      2. 2075925Domain d4gh4c_: 4gh4 C: [252215]
        automated match to d1fmd3_
    2. Domains for 4iv1:
      1. 2075922Domain d4iv1a_: 4iv1 A: [223403]
        automated match to d4iv3a_
      2. 2075923Domain d4iv1c_: 4iv1 C: [223404]
        automated match to d4iv3c_
    3. Domains for 4iv3:
      1. 2075926Domain d4iv3a_: 4iv3 A: [196862]
        automated match to d1zba1_
      2. 2075927Domain d4iv3c_: 4iv3 C: [196863]
        automated match to d1zba3_
    4. Domains for 5d8a:
      1. 2075928Domain d5d8aa_: 5d8a A: [277131]
        automated match to d1fmd1_
      2. 2075929Domain d5d8ac_: 5d8a C: [277140]
        automated match to d4iv1c_
  5. 2075930Foot-and-mouth disease virus [TaxId:12110] [188180] (3 PDB entries)
    1. Domains for 1zba:
      1. 2075931Domain d1zba1_: 1zba 1: [162437]
        automated match to d1qqp1_
      2. 2075932Domain d1zba3_: 1zba 3: [162438]
        automated match to d1bbt3_
    2. Domains for 1zbe:
      1. 2075933Domain d1zbe1_: 1zbe 1: [241128]
        automated match to d1fmd1_
      2. 2075934Domain d1zbe3_: 1zbe 3: [241129]
        automated match to d1fmd3_
    3. Domain for 5ne4:
  6. 2075935Foot-and-mouth disease virus [TaxId:12122] [255673] (1 PDB entry)
  7. 2075937Human coxsackievirus B3 [TaxId:12072] [194627] (1 PDB entry)
  8. 2075939Human echovirus 7 [TaxId:46018] [255678] (1 PDB entry)
  9. 2075942Human enterovirus 71 [TaxId:39054] [195913] (11 PDB entries)
    1. Domain for 3vbf:
    2. Domain for 3vbh:
    3. Domain for 3zfe:
    4. Domain for 4cdq:
    5. Domain for 4cdu:
    6. Domain for 4cdw:
    7. Domain for 4cdx:
    8. Domain for 4cew:
    9. Domain for 4cey:
    10. Domains for 4rqp:
      1. 2075956Domain d4rqpb_: 4rqp B: [261955]
        Other proteins in same PDB: d4rqpc_, d4rqpg_, d4rqpk_, d4rqpo_
        automated match to d3vbhc_
      2. 2075957Domain d4rqpf_: 4rqp F: [261954]
        Other proteins in same PDB: d4rqpc_, d4rqpg_, d4rqpk_, d4rqpo_
        automated match to d3vbhc_
      3. 2075958Domain d4rqpj_: 4rqp J: [261957]
        Other proteins in same PDB: d4rqpc_, d4rqpg_, d4rqpk_, d4rqpo_
        automated match to d3vbhc_
      4. 2075959Domain d4rqpn_: 4rqp N: [261961]
        Other proteins in same PDB: d4rqpc_, d4rqpg_, d4rqpk_, d4rqpo_
        automated match to d3vbhc_
      5. 2075960Domain d4rqpr_: 4rqp R: [261966]
        Other proteins in same PDB: d4rqpc_, d4rqpg_, d4rqpk_, d4rqpo_
        automated match to d3vbhc_
    11. Domains for 4rr3:
      1. 2075951Domain d4rr3b_: 4rr3 B: [267406]
        automated match to d3vbhc_
      2. 2075952Domain d4rr3f_: 4rr3 F: [267407]
        automated match to d3vbhc_
      3. 2075953Domain d4rr3j_: 4rr3 J: [267408]
        automated match to d3vbhc_
      4. 2075954Domain d4rr3n_: 4rr3 N: [267409]
        automated match to d3vbhc_
      5. 2075955Domain d4rr3r_: 4rr3 R: [267410]
        automated match to d3vbhc_
  10. 2075962Human rhinovirus 14 [TaxId:12131] [258112] (1 PDB entry)
  11. 2075965Human rhinovirus 2 [TaxId:12130] [256100] (1 PDB entry)
  12. 2275067Saffold virus [TaxId:434309] [318368] (2 PDB entries)
    1. Domains for 5cfc:
      1. 2275068Domain d5cfcb_: 5cfc B: [318369]
        automated match to d1tmf3_
      2. 2275139Domain d5cfca_: 5cfc A: [318440]
        automated match to d1tme1_
    2. Domains for 5cfd:
      1. 2275182Domain d5cfdb_: 5cfd B: [318483]
        automated match to d1tmf3_
      2. 2275292Domain d5cfda_: 5cfd A: [318593]
        automated match to d1tme1_
  13. 2292138Foot-and-mouth disease virus - type o [TaxId:12118] [335439] (1 PDB entry)

More info for Protein automated matches from b.121.4.1: Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Timeline for Protein automated matches from b.121.4.1: Picornaviridae-like VP (VP1, VP2, VP3 and VP4):