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(-) Description

Title :  CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS
 
Authors :  M. Mathieu, I. Petitpas, F. A. Rey
Date :  29 Apr 99  (Deposition) - 13 Apr 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Viral Capsid Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mathieu, I. Petitpas, J. Navaza, J. Lepault, E. Kohli, P. Pothier, B. V. Prasad, J. Cohen, F. A. Rey
Atomic Structure Of The Major Capsid Protein Of Rotavirus: Implications For The Architecture Of The Virion.
Embo J. V. 20 1485 2001
PubMed-ID: 11285213  |  Reference-DOI: 10.1093/EMBOJ/20.7.1485
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VIRAL CAPSID VP6
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector: BACULOVIRUS
    Gene: SEGMENT 6
    Organism Scientific: BOVINE ROTAVIRUS
    Organism Taxid: 129818
    Other Details: ONE MONOMER IN ASYMETRIC UNIT
    Strain: RF

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CA5Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:153 , CL A:502BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREHIS A:153 , ZN A:501BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWAREHOH A:874 , HOH A:890BINDING SITE FOR RESIDUE CA A 503
4AC4SOFTWAREASN A:266 , ASP A:286 , HOH A:794BINDING SITE FOR RESIDUE CA A 508
5AC5SOFTWAREGLN A:268 , GLU A:379 , HOH A:652 , HOH A:668 , HOH A:767 , HOH A:789 , HOH A:845BINDING SITE FOR RESIDUE CA A 601
6AC6SOFTWAREGLN A:47 , ASP A:62 , HOH A:681 , HOH A:779 , HOH A:783BINDING SITE FOR RESIDUE CA A 602
7AC7SOFTWARETHR A:151 , GLU A:340 , HOH A:628 , HOH A:886BINDING SITE FOR RESIDUE CA A 603
8ZNBAUTHORHIS A:153THE ZINC SITS ON A THREE-FOLD AXIS. THE ZINC BINDING SITE FORMED BY THREE SYMMETRICALLY-RELATED PLUS ONE WATER MOLECULE ON THE THREE-FOLD AXIS.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QHD)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:312 -Pro A:313

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QHD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QHD)

(-) Exons   (0, 0)

(no "Exon" information available for 1QHD)

(-) 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:398
 aligned with VP6_ROTRF | P04509 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:398
                             1                                                                                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
            VP6_ROTRF     - -MDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLIKLSGIKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANTQQFEHIVQLRRVLTTATITLLPDAERFSFPRVITSADGATTWYFNPVILRPNNVEIEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASETMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK 397
               SCOP domains -d1qhda1 A:1-148,A:333-397 vp6, the major capsid protein of group A rotavirus                                                                        d1qhda2 A:149-332 vp6, the major capsid protein of group A rotavirus                                                                                                                    d1qhda1 A:1-148,A:333-397                                         SCOP domains
               CATH domains -1qhdA02 A:1-158,A:329-397 Viral capsid alpha domain                                                                                                           1qhdA01 A:159-328  [code=2.60.120.170, no name defined]                                                                                                                   1qhdA02 A:1-158,A:329-397 Viral capsid alpha domain                   CATH domains
               Pfam domains -Rota_Capsid_VP6-1qhdA01 A:1-396                                                                                                                                                                                                                                                                                                                                                                             - Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh......hhh.hhhhhhhhhhhhhh...eeee........eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhh.hhhhhh......hhhhhhhhhhh.....eeee.......eeeeeeee........eeeeeeee..eeeeeeee.......hhheeeeeeeee.......eeeeeee..hhh...eeee......eeee.eee......eeeeee..eeeeeee...eeeee....eeeeeeeee......hhhhhh.........eeeeeeeeeeeeeee..........hhhhhhhhhhh..........hhh.hhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qhd A   0 xMDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLIKLSGIKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANTQQFEHIVQLRRVLTTATITLLPDAERFSFPRVITSADGATTWYFNPVILRPNNVEIEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASETMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK 397
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
                            |                                                                                                                                                                                                                                                                                                                                                                                                             
                            0-ACE
   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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Rota_Capsid_VP6] (1)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (VP6_ROTRF | P04509)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0039626    viral intermediate capsid    The intermediate layer of a triple concentric icosahedral capsid. Intermediate capsids are part of reoviridae virions.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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        VP6_ROTRF | P04509: 3gzu 3j9s

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