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(-) Description

Title :  PBCV-1 VIRUS CAPSID, QUASI-ATOMIC MODEL
 
Authors :  N. Nandhagopal, A. A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Graves, J. L. Van Etten, M. G. Rossmann
Date :  05 Jul 02  (Deposition) - 04 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  28.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1680x)
Keywords :  Icosahedral Virus Capsid, Beta Barrel, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nandhagopal, A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Graves, J. L. Van Etten, M. G. Rossmann
The Structure And Evolution Of The Major Capsid Protein Of A Large, Lipid Containing, Dna Virus.
Proc. Natl. Acad. Sci. Usa V. 99 14758 2002
PubMed-ID: 12411581  |  Reference-DOI: 10.1073/PNAS.232580699
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PBCV-1 VIRUS CAPSID
    Chains: A, B, C
    Fragment: VIRUS CAPSID
    Organism Scientific: PARAMECIUM BURSARIA CHLORELLA VIRUS 1
    Organism Taxid: 10506
    Other Details: VIRUS INFECTS CHLORELLA ALGAE, WHICH ARE SYMBIONTS WITH PARAMECIUM BURSARIA

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1680x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1M4X)

(-) Sites  (0, 0)

(no "Site" information available for 1M4X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M4X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M4X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M4X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M4X)

(-) Exons   (0, 0)

(no "Exon" information available for 1M4X)

(-) 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:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1m4xa_ A: PBCV-1 virus capsid, quasi-atomic model                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee...........eeeee......eeeeeeeeeeee.........hhhhhheeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..hhhhhhhhhhee.hhh....eeeeeee........ee..ee.......eeeeeeeeeeehhhhhhhhhhh.eeeeeeeeeeeeee..........eeeee.....eeeeeeeeee...............................hhhhh...hhhhh...eeeeee..ee....eehhhhhhhhhhhh........eeeee.............ee.hhh..eeeeee..eeee...hhhhhh.....eee.hhhhh.eeeeeeeeeeeeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4x A  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQAAQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   


Chain B from PDB  Type:PROTEIN  Length:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1m4xb_ B: PBCV-1 virus capsid, quasi-atomic model                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee...........eeeee......eeeeeeeeeeee.........hhhhhheeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..hhhhhhhhhhee.hhh....eeeeeee........ee..ee.......eeeeeeeeeeehhhhhhhhhhh.eeeeeeeeeeeeee..........eeeee.....eeeeeeeeee...............................hhhhh...hhhhh...eeeeee..ee....eehhhhhhhhhhhh........eeeee.............ee.hhh..eeeeee..eeee...hhhhhh.....eee.hhhhh.eeeeeeeeeeeeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4x B  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQAAQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   


Chain C from PDB  Type:PROTEIN  Length:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1m4xc_ C: PBCV-1 virus capsid, quasi-atomic model                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Capsid_NCLDV-1m4xC01 C:196-433                                                                                                                                                                                                                ---- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Capsid_NCLDV-1m4xC02 C:196-433                                                                                                                                                                                                                ---- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Capsid_NCLDV-1m4xC03 C:196-433                                                                                                                                                                                                                ---- Pfam domains (3)
         Sec.struct. author ............eeeeeee...........eeeee......eeeeeeeeeeee.........hhhhhheeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..hhhhhhhhhhee.hhh....eeeeeee........ee..ee.......eeeeeeeeeeehhhhhhhhhhh.eeeeeeeeeeeeee..........eeeee.....eeeeeeeeee...............................hhhhh...hhhhh...eeeeee..ee....eehhhhhhhhhhhh........eeeee.............ee.hhh..eeeeee..eeee...hhhhhh.....eee.hhhhh.eeeeeeeeeeeeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4x C  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQAAQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434
   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: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1M4X)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Capsid_NCLDV] (2)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (MCP_PBCV1 | P30328)
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

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

UniProtKB/Swiss-Prot
        MCP_PBCV1 | P30328: 1j5q 1m3y 3kk5

(-) Related Entries Specified in the PDB File

1j5q CRYSTAL STRUCTURE OF PBCV-1 CAPSID PROTEIN
1m3y CRYSTAL STRUCTURE OF PBCV-1 CAPSID PROTEIN