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(-) Description

Title :  VIRUS MODEL OF BROME MOSAIC VIRUS (FIRST HALF DATA SET)
 
Authors :  Z. Wang, C. Hryc, B. Bammes, P. V. Afonine, J. Jakana, D. H. Chen, X. Liu, M C. Kao, S. J. Ludtke, M. F. Schmid, P. D. Adams, W. Chiu
Date :  18 Jul 14  (Deposition) - 10 Sep 14  (Release) - 18 May 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Capsid Protein, Bmv, Beta Barrel, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Wang, C. F. Hryc, B. Bammes, P. V. Afonine, J. Jakana, D. H. Chen, X. Liu, M. L. Baker, C. Kao, S. J. Ludtke, M. F. Schmid, P. D. Adams, W. Chi
An Atomic Model Of Brome Mosaic Virus Using Direct Electron Detection And Real-Space Optimization.
Nat Commun V. 5 4808 2014
PubMed-ID: 25185801  |  Reference-DOI: 10.1038/NCOMMS5808

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B, C
    Organism Common: BMV
    Organism Scientific: BROME MOSAIC VIRUS
    Organism Taxid: 12302
    Synonym: CP, COAT PROTEIN

 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 3J7M)

(-) Sites  (0, 0)

(no "Site" information available for 3J7M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3J7M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg B:142 -Gly B:143
2Val B:187 -Tyr B:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J7M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J7M)

(-) Exons   (0, 0)

(no "Exon" information available for 3J7M)

(-) 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_BMV | P03602 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:149
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180         
            CAPSD_BMV    41 KAIKAIAGYSISKWEASSDAITAKATNAMSITLPHELSSEKNKELKVGRVLLWLGLLPSVAGRIKACVAEKQAQAEAAFQVALAVADSSKEVVAAMYTDAFRGATLGDLLNLQIYLYASEAVPAKAVVVHLEVEHVRPTFDDFFTPVYR 189
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeee.........eeee................eeeeeeeeee.......eeeeee.....hhhhhhh....ee.......eee.......hhhhhhh.eeeeee........eeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7m A  41 KAIKAIAGYSISKWEASSDAITAKATNAMSITLPHELSSEKNKELKVGRVLLWLGLLPSVAGRIKACVAEKQAQAEAAFQVALAVADSSKEVVAAMYTDAFRGATLGDLLNLQIYLYASEAVPAKAVVVHLEVEHVRPTFDDFFTPVYR 189
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain B from PDB  Type:PROTEIN  Length:165
 aligned with CAPSD_BMV | P03602 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:165
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184     
            CAPSD_BMV    25 ARVQPVIVEPLAAGQGKAIKAIAGYSISKWEASSDAITAKATNAMSITLPHELSSEKNKELKVGRVLLWLGLLPSVAGRIKACVAEKQAQAEAAFQVALAVADSSKEVVAAMYTDAFRGATLGDLLNLQIYLYASEAVPAKAVVVHLEVEHVRPTFDDFFTPVYR 189
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eee................eee....hhhhh.hhhhh.eeeeeeee.........eeeeee......hhhhhhh...ee......eee........hhhhhhh.eeeeee..........eeeeeeee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7m B  25 ARVQPVIVEPLAAGQGKAIKAIAGYSISKWEASSDAITAKATNAMSITLPHELSSEKNKELKVGRVLLWLGLLPSVAGRIKACVAEKQAQAEAAFQVALAVADSSKEVVAAMYTDAFRGATLGDLLNLQIYLYASEAVPAKAVVVHLEVEHVRPTFDDFFTPVYR 189
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184     


Chain C from PDB  Type:PROTEIN  Length:164
 aligned with CAPSD_BMV | P03602 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:164
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    
            CAPSD_BMV    26 RVQPVIVEPLAAGQGKAIKAIAGYSISKWEASSDAITAKATNAMSITLPHELSSEKNKELKVGRVLLWLGLLPSVAGRIKACVAEKQAQAEAAFQVALAVADSSKEVVAAMYTDAFRGATLGDLLNLQIYLYASEAVPAKAVVVHLEVEHVRPTFDDFFTPVYR 189
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................eee..........ee................eeeeeeeeeee.......eeeee........hhhhhh...........eeee......eehhhhhh..eeeee........eeee..eee..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7m C  26 RVQPVIVEPLAAGQGKAIKAIAGYSISKWEASSDAITAKATNAMSITLPHELSSEKNKELKVGRVLLWLGLLPSVAGRIKACVAEKQAQAEAAFQVALAVADSSKEVVAAMYTDAFRGATLGDLLNLQIYLYASEAVPAKAVVVHLEVEHVRPTFDDFFTPVYR 189
                                    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  (0, 0)

(no "SCOP Domain" information available for 3J7M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J7M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J7M)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CAPSD_BMV | P03602)
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:0044165    host cell endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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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  Cis Peptide Bonds
    Arg B:142 - Gly B:143   [ RasMol ]  
    Val B:187 - Tyr B:188   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_BMV | P03602: 1js9 1yc6 3j7l 3j7n

(-) Related Entries Specified in the PDB File

3j7l 3j7n