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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SALT STABLE COWPEA CHOLOROTIC MOTTLE VIRUS AT 2.7 ANGSTROMS RESOLUTION.
 
Authors :  B. Bothner, J. A. Speir, C. Qu, D. A. Willits, M. J. Young, J. E. Johnson
Date :  05 Apr 05  (Deposition) - 21 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Mutant Virus Capsid Structure, Icosahedral Particle, Stablizing Mutation, Stable Mutant, Beta Hexamer, Beta Barrel, Bromovirus, Point Mutation, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Speir, B. Bothner, C. Qu, D. A. Willits, M. J. Young, J. E. Johnson
Enhanced Local Symmetry Interactions Globally Stabilize A Mutant Virus Capsid That Maintains Infectivity And Capsid Dynamics.
J. Virol. V. 80 3582 2006
PubMed-ID: 16537626  |  Reference-DOI: 10.1128/JVI.80.7.3582-3591.2006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: VIGNA UNGUICULATA
    Expression System Common: COWPEA
    Expression System Strain: CALIFORNIA BLACKEYE
    Expression System Taxid: 3917
    Expression System Vector Type: RNA
    Gene: RNA4
    Mutation: YES
    Organism Scientific: COWPEA CHLOROTIC MOTTLE VIRUS
    Organism Taxid: 12303
    Synonym: CAPSID PROTEIN, CP

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ZA7)

(-) Sites  (0, 0)

(no "Site" information available for 1ZA7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZA7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZA7)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZA7)

(-) 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:151
 aligned with CAPSD_CCMV | P03601 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:151
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 
           CAPSD_CCMV    40 QGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
               SCOP domains d1za7a_ A: automated matches                                                                                                                            SCOP domains
               CATH domains 1za7A00 A:40-190  [code=2.60.120.220, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee........eeeee...hhhhh..hhhhh.eeeeeeeeee.......eeeeeee...hhhhhhhhh...ee......eeee.......hhhhhhhheeeeeee........eeeeeeeeee.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1za7 A  40 QGRAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLAADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 


Chain B from PDB  Type:PROTEIN  Length:165
 aligned with CAPSD_CCMV | P03601 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:165
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     
           CAPSD_CCMV    26 RVVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
               SCOP domains d1za7b_ B: automated matches                                                                                                                                          SCOP domains
               CATH domains -----------1za7B01 B:37-190  [code=2.60.120.220, no name defined]                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeeeeee........eeeee...hhhhh..hhhhh.eeeeeeeeee.......eeeeeee...hhhhhhhhh...ee......eeee.......hhhhhhhheeeeeee........eeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1za7 B  26 RVVQPVIVEPIASGQGRAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLAADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     


Chain C from PDB  Type:PROTEIN  Length:165
 aligned with CAPSD_CCMV | P03601 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:165
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     
           CAPSD_CCMV    26 RVVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
               SCOP domains d1za7c_ C: automated matches                                                                                                                                          SCOP domains
               CATH domains -----------1za7C01 C:37-190  [code=2.60.120.220, no name defined]                                                                                                     CATH domains
           Pfam domains (1) Bromo_coat-1za7C01 C:26-189                                                                                                                                         - Pfam domains (1)
           Pfam domains (2) Bromo_coat-1za7C02 C:26-189                                                                                                                                         - Pfam domains (2)
           Pfam domains (3) Bromo_coat-1za7C03 C:26-189                                                                                                                                         - Pfam domains (3)
         Sec.struct. author ........................eeeeeeeee........eeeee...hhhhh..hhhhh.eeeeeeeeee.......eeeeeee...hhhhhhhhh...ee......eeee.......hhhhhhhheeeeeee........eeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1za7 C  26 RVVQPVIVEPIASGQGRAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLAADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185
   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  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CAPSD_CCMV | P03601)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0039617    T=3 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
    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:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_CCMV | P03601: 1cwp

(-) Related Entries Specified in the PDB File

1cwp THIS IS THE CRYSTAL STRUCTURE OF WILD-TYPE COWPEA CHLOROTIC MOTTLE VIRUS AT 3.2 ANSTROMS RESOLUTION.