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(-) Description

Title :  CRYSTAL STRUCTURE OF EMPTY COXSACKIEVIRUS A16 PARTICLE
 
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 :  26 Jun 15  (Deposition) - 26 Aug 15  (Release) - 30 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (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 - VP0
    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

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (60x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2K1Ligand/IonPOTASSIUM ION
3SPH1Ligand/IonSPHINGOSINE
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K-1Ligand/IonPOTASSIUM ION
3SPH60Ligand/IonSPHINGOSINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:112 , LEU A:113 , MET A:114 , TYR A:155 , MET A:195 , ASN A:228 , MET A:230binding site for residue SPH A 301
2AC2SOFTWAREGLN A:189 , VAL C:20binding site for residue K A 302
3AC3SOFTWAREARG A:236binding site for residue CL A 303
4AC4SOFTWAREHIS A:257 , VAL A:258 , GLN B:44binding site for residue CL A 304
5AC5SOFTWAREPRO B:232 , TYR B:233binding site for residue CL B 401
6AC6SOFTWARELYS B:138 , SER B:139binding site for residue CL B 402
7AC7SOFTWARETHR B:137binding site for residue CL B 403
8AC8SOFTWAREASN B:15 , LYS B:34binding site for residue CL B 404
9AC9SOFTWAREGLY C:91 , TRP C:111 , ALA C:181binding site for residue CL C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C9A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe B:151 -Pro B:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C9A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C9A)

(-) Exons   (0, 0)

(no "Exon" information available for 5C9A)

(-) 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:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.....ee...................hhhhh.....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
                 5c9a A   2 DPIADMISLTALQVLPTAANTEASSHRVVPALQAAETGASSNASDKNLIETRCVLNHHSTQETAIGNFFSRAGLVSIITMPTTGTQNTDGYVNWDIDLMGYAQLRRKCELFTYMRFDAEFTFVVAKPNGELVPQLLQYMYVPPGAPKPTSRDSFAWQTATNPSVFVKMTDPPAQVSVPFMSPASAYQWFYDGYPTFGEHLQANDLDYGQCPNNMMGTFSIRTVGIEKSPHSITLRVYMRIKHVRAWIPRPLRNQPYLFKTNPNYKGNDIKCTSTSRDKITTL 297
                                  ||21        31      ||45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  
                                  8|                 38|                                                                                                                                                                                                                                                              
                                  19                  43                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhh.......ee..................eee..eee........ee.hhh..................hhhhh...eeeeeeee......eeeeehhhhh.hhhhhhhhhheeeeeeeeeeeee.......eeeeeeeeee..................hhhhhhhhhhhee..hhhhh....hhhhhhhh.eeeee.....eeeeee................eeeeeeeeeeee........eeeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c9a B  11 GSHENSNSASEGSTINYTTINYYKDAYAASAGRQDMSQDPKKFTDPVMDVSDRVAQLTIGNSTITTQEAANIVIAYGEWPEYCPDTDATAVDKPTRPDVSVNRFFTLDTKSWAKDSKGWYWKFPDVLTEVGVFGQNAQFHYLYRSGFCVHVQCNASKFHQGALLVAVLPEYVLGTIAGGTGNENSHPPYATTQPGQVGAVLTHPYVLDAGIPLSQLTVCPHQWINLRTNNCATIIVPYMNTVPFDSALNHCNFGLLVIPVVPLDFNTGATSEIPITVTIAPMCAEFAGLRQAVKQ 323
                                    20        30        40        50        60|       88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318     
                                                                            60|                                                                                                                                                                                                                                                    
                                                                             79                                                                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee...............ee.hhhhhhh..ee...........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
                 5c9a 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
   Legend:   → Mismatch (orange background)
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  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 5C9A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C9A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C9A)

(-) Gene Ontology  (36, 36)

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 Related Entries

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

UniProtKB/Swiss-Prot
        I3W9E1_9ENTO | I3W9E1: 5c8c
UniProtKB/TrEMBL
        I3W9E1_9ENTO | I3W9E1: 4jgy 4jgz 5abj 5c4w

(-) Related Entries Specified in the PDB File

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