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(-) Description

Title :  STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MOTTLE VIRUS DETERMINED BY X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY
 
Authors :  J. A. Speir, J. E. Johnson, S. Munshi, G. Wang, S. Timothy, T. S. Baker
Date :  22 May 95  (Deposition) - 22 May 95  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (60x)
Keywords :  Bromovirus, Icosahedral Virus, Virus/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Speir, S. Munshi, G. Wang, T. S. Baker, J. E. Johnson
Structures Of The Native And Swollen Forms Of Cowpea Chlorotic Mottle Virus Determined By X-Ray Crystallography And Cryo-Electron Microscopy.
Structure V. 3 63 1995
PubMed-ID: 7743132  |  Reference-DOI: 10.1016/S0969-2126(01)00135-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C
    Organism Scientific: COWPEA CHLOROTIC MOTTLE VIRUS
    Organism Taxid: 12303
    Other Details: COWPEA PLANT
    Synonym: CCMV
    Variant: CALIFORNIA BLACKEYE
 
Molecule 2 - RNA (5'-R(*AP*UP*AP*U)-3')
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*AP*U)-3')
    Chains: E
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (60x): ABCDEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1CWP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CWP)

(-) 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:149
 aligned with CAPSD_CCMV | P03601 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:149
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181         
           CAPSD_CCMV    42 KAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
               SCOP domains d1cwpa_ A: Cucumovirus coat protein                                                                                                                   SCOP domains
               CATH domains 1cwpA00 A:42-190  [code=2.60.120.220, no name defined]                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee.......eeeee.....hhh..hhhhh.....eee...........eeeeeee....hhhhhhh.............eee........hhhhhhheeeeeee.........eeeeeeeee...hhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cwp A  42 KAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLAADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181         


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with CAPSD_CCMV | P03601 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:164
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
           CAPSD_CCMV    27 VVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
               SCOP domains d1cwpb_ B: Cucumovirus coat protein                                                                                                                                  SCOP domains
               CATH domains ----------1cwpB01 B:37-190  [code=2.60.120.220, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeeeee........eeeeee....hhhh.hhhhh.....eeeeee........eeeeeee....hhhhhhh.............eee........hhhhhhheeeeeee.........eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cwp B  27 VVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLAADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    


Chain C from PDB  Type:PROTEIN  Length:164
 aligned with CAPSD_CCMV | P03601 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:164
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
           CAPSD_CCMV    27 VVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
               SCOP domains d1cwpc_ C: Cucumovirus coat protein                                                                                                                                  SCOP domains
               CATH domains ----------1cwpC01 C:37-190  [code=2.60.120.220, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.........eeeeeeeee.......eeeeee.........hhhhh.....eeeeeee.......eeeeeee....hhhhhhh............eeee........hhhhhhheeeeeee........eeeeeeeeee...hhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cwp C  27 VVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLAADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY 190
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    


Chain D from PDB  Type:RNA  Length:4
                                    
                 1cwp D 201 AUAU 204


Chain E from PDB  Type:RNA  Length:2
                                  
                 1cwp E 201 AU 202


Chain F from PDB  Type:RNA  Length:4
                                    
                 1cwp F 201 AUAU 204
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "Pfam Domain" information available for 1CWP)

(-) 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: 1za7

(-) Related Entries Specified in the PDB File

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