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(-) Description

Title :  CRYSTAL STRUCTURE OF COXSACKIEVIRUS A16
 
Authors :  J. Ren, X. Wang, L. Zhu, Z. Hu, Q. Gao, P. Yang, X. Li, J. Wang, X. Shen, E. E. Z. Rao, D. I. Stuart
Date :  18 Jun 15  (Deposition) - 26 Aug 15  (Release) - 30 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Hand-Foot-And-Mouth Disease, Immunogenicity, Picornavirus, Icosahedral Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ren, X. Wang, L. Zhu, Z. Hu, Q. Gao, P. Yang, X. Li, J. Wang, X. Shen, E. E. Fry, Z. Rao, D. I. Stuart
Structures Of Coxsackievirus A16 Capsids With Native Antigenicity: Implications For Particle Expansion, Receptor Binding, And Immunogenicity.
J. Virol. V. 89 10500 2015
PubMed-ID: 26269176  |  Reference-DOI: 10.1128/JVI.01102-15

(-) Compounds

Molecule 1 - VP1
    Cell Line: VERO
    Chains: A
    Organism Scientific: COXSACKIEVIRUS A16
    Organism Taxid: 31704
 
Molecule 2 - VP2
    Cell Line: VERO
    Chains: B
    Organism Scientific: COXSACKIEVIRUS A16
    Organism Taxid: 31704
 
Molecule 3 - VP3
    Cell Line: VERO
    Chains: C
    Organism Scientific: COXSACKIEVIRUS A16
    Organism Taxid: 31704
 
Molecule 4 - VP4
    Cell Line: VERO
    Chains: D
    Organism Scientific: COXSACKIEVIRUS A16
    Organism Taxid: 31704

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (60x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2K2Ligand/IonPOTASSIUM ION
3NA1Ligand/IonSODIUM ION
4SPH1Ligand/IonSPHINGOSINE
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K-1Ligand/IonPOTASSIUM ION
3NA-1Ligand/IonSODIUM ION
4SPH60Ligand/IonSPHINGOSINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:112 , LEU A:113 , MET A:114 , TYR A:155 , ASN A:228 , MET A:230binding site for residue SPH A 301
2AC2SOFTWARETHR A:28 , ALA A:29 , ASN A:31 , ASN A:71binding site for residue K A 302
3AC3SOFTWAREVAL A:44 , PRO A:45 , LEU A:47 , GLN A:48 , ALA D:65 , PRO D:67binding site for residue NA A 303
4AC4SOFTWAREARG A:236binding site for residue CL A 304
5AC5SOFTWAREGLN A:189 , VAL C:20 , SER C:21binding site for residue K A 305
6AC6SOFTWAREHIS B:162 , PRO B:163 , TYR B:164binding site for residue CL B 301
7AC7SOFTWAREGLY C:91 , TRP C:111 , ALA C:181binding site for residue CL C 301
8AC8SOFTWAREGLY C:1binding site for residue CL C 302
9AC9SOFTWAREASN D:15 , LYS D:34binding site for residue CL D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C4W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C4W)

(-) Exons   (0, 0)

(no "Exon" information available for 5C4W)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee.....................eehhhhh.....hhhhhh..........hhhhhhhhhhh..eeeeeeee..........eeeee.....hhhhhhhhh.eeeeeeeeeeeeeee.........eeeeeee...........hhhhhh....eeeee.....eeeee........ee............hhhhh.....hhhhh..eeeeee.........eeeeeeeeeeeeeeeee.................................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c4w A   2 DPIADMIRSLTALQVLPTAANTEASSHRLGTGVVPALQAAETGASSNASDKNLIETRCVLNHHSTQETAIGNFFSRAGLVSIITMPTTGTQNTDGYVNWDIDLMGYAQLRRKCELFTYMRFDAEFTFVVAKPNGELVPQLLQYMYVPPGAPKPTSRDSFAWQTATNPSVFVKMTDPPAQVSVPFMSPASAYQWFYDGYPTFGEHLQANDLDYGQCPNNMMGTFSIRTVGIEKSPHSITLRVYMRIKHVRAWIPRPLRNQPYLFKTNPNYKGNDIKCTSTSRDKITTL 297
                                  ||20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
                                  8|                                                                                                                                                                                                                                                                                       
                                  18                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeee......ee.hhh..................hhhhh...ee...eee......eeeeehhhhh.hhhhhhhhhheeeeeeeeeeeee.......eeeeeeeeee..................hhhhhhhhhhhee..hhhhh....hhhhhhhh.eeeee.....eeeeee................eeeeeeeeeeee........eeeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c4w B  10 SDRVAQLTIGNSTITTQEAANIVIAYGEWPEYCPDTDATAVDKPTRPDVSVNRFFTLDTKSWAKDSKGWYWKFPDVLTEVGVFGQNAQFHYLYRSGFCVHVQCNASKFHQGALLVAVLPEYVLGTIAGGTGNENSHPPYATTQPGQVGAVLTHPYVLDAGIPLSQLTVCPHQWINLRTNNCATIIVPYMNTVPFDSALNHCNFGLLVIPVVPLDFNTGATSEIPITVTIAPMCAEFAGLRQAVKQ 254
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249     


Chain C from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................ee.hhhhhhh..ee.....hhhhh.hhhhhhheeee.......eeeeee......hhhhhhhhhhhhh.eeeee..eeeeeee........eeeeeee........hhhhhh..eeeeee.....eeeeee........ee....hhhhhhh..eeeeee............eeeeeeeeee....eeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c4w C   1 GIPTELKPGTNQFLTTDDGVSAPILPGFHPTPPIHIPGEVHNLLEICRVETILEVNNLKTNETTPMQRLCFPVSVQSKTGELCAAFRADPGRDGPWQSTILGQLCRYYTQWSGSLEVTFMFAGSFMATGKMLIAYTPPGGNVPADRITAMLGTHVIWDFGLQSSVTLVVPWISNTHYRAHARAGYFDYYTTGIITIWYQTNYVVPIGAPTTAYIVALAAAQDNFTMKLCKDTEDIEQTANIQ 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  


Chain D from PDB  Type:PROTEIN  Length:58
                                                                                          
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhh.......ee.hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 5c4w D  12 SHENSNSASEGSTINYTTINYYKDAYAASAGRQDMSQDPKKFTDPVMDVIHEMAPPLK  69
                                    21        31        41        51        61
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5C4W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C4W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C4W)

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        I3W9E1_9ENTO | I3W9E1: 5c8c
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        I3W9E1_9ENTO | I3W9E1: 4jgy 4jgz 5abj 5c9a

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