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(-) Description

Title :  SWINE VESICULAR DISEASE VIRUS COAT PROTEIN
 
Authors :  N. Verdaguer, M. A. Jimenez-Clavero, I. Fita, V. Ley
Date :  17 Sep 02  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Swine Vesicular Disease Virus, Svdv Coat Protein, Enterovirus, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Verdaguer, M. A. Jimenez-Clavero, I. Fita, V. Ley
Structure Of Swine Vesicular Disease Virus: Mapping Of Changes Occurring During Adaptation Of Human Coxsackie B5 Virus To Infect Swine
J. Virol. V. 77 9780 2003
PubMed-ID: 12941886  |  Reference-DOI: 10.1128/JVI.77.18.9780-9789.2003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYPROTEIN
    Chains: A
    Fragment: SVDV COAT PROTEIN VP1
    Organism Scientific: SWINE VESICULAR DISEASE VIRUS
    Organism Taxid: 12075
    Strain: ISOLATE (SPA-2-'93)
 
Molecule 2 - POLYPROTEIN CAPSID PROTEIN
    Chains: B
    Fragment: SVDV COAT PROTEIN VP2
    Organism Scientific: SWINE VESICULAR DISEASE VIRUS
    Organism Taxid: 12075
    Strain: ISOLATE (SPA-2-'93)
 
Molecule 3 - POLYPROTEIN CAPSID PROTEIN
    Chains: C
    Fragment: SVDV COAT PROTEIN VP3
    Organism Scientific: SWINE VESICULAR DISEASE VIRUS
    Organism Taxid: 12075
    Strain: ISOLATE (SPA-2-'93)
 
Molecule 4 - POLYPROTEIN CAPSID PROTEIN
    Chains: D
    Fragment: SVDV COAT PROTEIN VP4
    Organism Scientific: SWINE VESICULAR DISEASE VIRUS
    Organism Taxid: 12075
    Strain: ISOLATE (SPA-2-'93)

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SPL1Ligand/IonOCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
1SPL60Ligand/IonOCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:94 , PHE A:114 , LEU A:116 , LEU A:118 , TYR A:145 , MET A:180 , ILE A:182 , ILE A:185 , SER A:192 , MET A:193 , LEU A:212 , MET A:215 , ALA C:24BINDING SITE FOR RESIDUE SPL A 284

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MQT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MQT)

(-) 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:271
 aligned with Q8B8X4_9ENTO | Q8B8X4 from UniProtKB/TrEMBL  Length:851

    Alignment length:271
                                   590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850 
         Q8B8X4_9ENTO   581 RVADTVGSGPVNSESIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESTVENFLCRSACVFYTTYKNHDSDGDNFAYWVINARQVAQLRRKLEMFTYARFDLELTFVITSTQEQSTTQGQDTPVLTHQIMYVPPGGPVPTKVNSYSWQTSTNPSVFWTEGNAPPRMSIPFIGIGNAYSMFYDGWARFDKQGTYGISTLNSMGTLYMRHVNGGGPGPIVSTVRIYFKPKHVKTWVPRPPRLCQYKKAGNVNFIPTSVTEGRTDITTMKTT 851
               SCOP domains d1mqta_ A: Swine vesicular disease virus coat proteins                                                                                                                                                                                                                          SCOP domains
               CATH domains 1mqtA00 A:13-283  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eehhhhh.....................hhhhhhhhhhh..eeeeeeeee.........eeee.....hhhhhhhhh.eeeeeeeeeeeeeeeeee.............eeeeeee...........hhhhhh....eeeee......eeee........ee...............hhhhh....eeeeee........eeeeeeeee.eeeeeeeee.................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mqt A  13 RVADTVGSGPVNSESIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESTVENFLCRSACVFYTTYKNHDSDGDNFAYWVINARQVAQLRRKLEMFTYARFDLELTFVITSTQEQSTTQGQDTPVLTHQIMYVPPGGPVPTKVNSYSWQTSTNPSVFWTEGNAPPRMSIPFIGIGNAYSMFYDGWARFDKQGTYGISTLNSMGTLYMRHVNGGGPGPIVSTVRIYFKPKHVKTWVPRPPRLCQYKKAGNVNFIPTSVTEGRTDITTMKTT 283
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with Q8B8X4_9ENTO | Q8B8X4 from UniProtKB/TrEMBL  Length:851

    Alignment length:254
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326    
         Q8B8X4_9ENTO    77 GYSDRVRSITLGNSTITTQECANVVVGYGVWPAYLKDEEATAEDQPTQPDVATCRFYTLESVMWQQGSPGWWWKFPDALSNMGLFGQNMQYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGCATLANKPDPKSLSKGEIASTFESQNSTGETAVQANVINAGMGVGVGNLTIFPHQWINLRTNNSATIVMPYINSVPMDNMFRHNNFTLMVIPFAPLSYSAGATTYVPITVTVAPMCAEYNGLRLAGKQ 330
               SCOP domains d1mqt.1 D:,B: Swine vesicular disease virus coat proteins                                                                                                                                                                                                      SCOP domains
               CATH domains 1mqtB00 B:8-261  [code=2.60.120.20, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..eeee.......ee......................hhhhh...ee...eee......eeee.......hhhhhhhhhheeeeeeeeeeeeee......eeeeeeeee..............hhhhhh.....ee..............hhhhh....hhhhhhhh.eeeee.....eeeeee.................eeeeeeeeeee........eeeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mqt B   8 GYSDRVRSITLGNSTITTQECANVVVGYGVWPAYLKDEEATAEDQPTQPDVATCRFYTLESVMWQQGSPGWWWKFPDALSNMGLFGQNMQYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGCATLANKPDPKSLSKGEIASTFESQNSTGETAVQANVINAGMGVGVGNLTIFPHQWINLRTNNSATIVMPYINSVPMDNMFRHNNFTLMVIPFAPLSYSAGATTYVPITVTVAPMCAEYNGLRLAGKQ 261
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257    


Chain C from PDB  Type:PROTEIN  Length:238
 aligned with Q8B8X4_9ENTO | Q8B8X4 from UniProtKB/TrEMBL  Length:851

    Alignment length:238
                                   340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560        
         Q8B8X4_9ENTO   331 GLPTLATPGSNQFLTSDDFQSPSAMPQFDVTPEMDIPGQVNNLMEIAEVDSVVPVNNTEGKEMSIEAYQIPVQSNPTNGSQVFGFPLTPGASSVLNRTLLGEILNYYAHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAPTTRKEAMLGTHVIWDVGLQSSCVLCIPWISQTHYRYVVMDEYTAGGYITCWYQTNIVVPADAQSDCKILCFVSACNDFSVRMLKDTPFIKQDNFFQ 568
               SCOP domains d1mqtc_ C: Swine vesicular disease virus coat proteins                                                                                                                                                                                         SCOP domains
               CATH domains 1mqtC00 C:1-238  [code=2.60.120.20, no name defined]                                                                                                                                                                                           CATH domains
           Pfam domains (1) ---------------------------Rhv-1mqtC01 C:28-198                                                                                                                                                       ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Rhv-1mqtC02 C:28-198                                                                                                                                                       ---------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------Rhv-1mqtC03 C:28-198                                                                                                                                                       ---------------------------------------- Pfam domains (3)
         Sec.struct. author ......................................ee..hhhhhh...........hhhhhhhhhheee........eeeeee...........hhhhhhhh.eeeee..eeeeeee......eeeeeeeee........hhhhhh..eeeeee.....eeeeee........ee...hhhhh..eeeeeeeeeee........eeeeeeeee....eeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mqt C   1 GLPTLATPGSNQFLTSDDFQSPSAMPQFDVTPEMDIPGQVNNLMEIAEVDSVVPVNNTEGKEMSIEAYQIPVQSNPTNGSQVFGFPLTPGASSVLNRTLLGEILNYYAHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAPTTRKEAMLGTHVIWDVGLQSSCVLCIPWISQTHYRYVVMDEYTAGGYITCWYQTNIVVPADAQSDCKILCFVSACNDFSVRMLKDTPFIKQDNFFQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain D from PDB  Type:PROTEIN  Length:55
 aligned with Q8B8X4_9ENTO | Q8B8X4 from UniProtKB/TrEMBL  Length:851

    Alignment length:68
                                    11        21        31        41        51        61        
         Q8B8X4_9ENTO     2 GAQVSTQKTGAHETSLNAAGNSVIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMVKSMPALN  69
               SCOP domains d1mqt.1 D:             ,B: Swine vesicular disease virus coat protei SCOP domains
               CATH domains 1mqtD00 D:             2-69 Rhinovirus 14, subunit 4                 CATH domains
               Pfam domains Pico_P1A-1             mqtD01 D:2-69                                 Pfam domains
         Sec.struct. author ..eeee....-------------.eeee.....hhhhh.............................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1mqt D   2 GAQVSTQKTG-------------IHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMVKSMPALN  69
                                    11         -   |    31        41        51        61        
                                    11            25
   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  (1, 3)

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

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Clan: no clan defined [family: Pico_P1A] (41)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8B8X4_9ENTO | Q8B8X4)
molecular function
    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.
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:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1cov COXSACKIEVIRUS B3 COAT PROTEIN