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(-) Description

Title :  CRYSTAL STRUCTURE OF IBDV T1 VIRUS-LIKE PARTICLE REVEALS A MISSING LINK IN ICOSAHEDRAL VIRUSES EVOLUTION
 
Authors :  F. Coulibaly, C. Chevalier, I. Gutsche, J. Pous, S. Bressanelli, J. Navaza, B. Delmas, F. A. Rey
Date :  12 Nov 04  (Deposition) - 05 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  J
Biol. Unit 1:  J  (60x)
Keywords :  Virus, Non-Enveloped Icosahedral Viruses, Double-Stranded Rna Virus Protein, Birnavirus, Transcriptase Machinery, Hydrolase, Membrane Translocation Activity, Evolution, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Coulibaly, C. Chevalier, I. Gutsche, J. Pous, J. Navaza, S. Bressanelli, B. Delmas, F. A. Rey
The Birnavirus Crystal Structure Reveals Structural Relationships Among Icosahedral Viruses.
Cell(Cambridge, Mass. ) V. 120 761 2005
PubMed-ID: 15797378  |  Reference-DOI: 10.1016/J.CELL.2005.01.009

(-) Compounds

Molecule 1 - MAJOR STRUCTURAL PROTEIN VP2
    Chains: J
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 1-441
    Organism Common: IBDV
    Organism Scientific: INFECTIOUS BURSAL DISEASE VIRUS
    Organism Taxid: 10995
    Other Details: VACCINE STRAIN (MERIAL)
    Strain: CT
    Synonym: IBDV VP2 SUBVIRAL PARTICLE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : J
Biological Unit 1 (60x): J

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1WCD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WCD)

(-) 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 J from PDB  Type:PROTEIN  Length:421
 aligned with POLS_IBDVC | P15480 from UniProtKB/Swiss-Prot  Length:1012

    Alignment length:421
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430 
           POLS_IBDVC    11 IVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQSNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLPGGVYALNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQPGGVTITLFSANIDAITSLSVGGELVFQTSVHGLVLGATIYLIGFDGTTVITRAVAANNGLTTGTDNLMPFNLVISTNEITQPITSIKLEIVTSKSGGQAGDQMSWSAKGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVAD 431
               SCOP domains d1wcdj1 J:11-431 Birnavirus VP2                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh............eeeeeeeeeeee......eeeee.......eeeeeeee.....eeeeeeee...hhhh.eeeeeeeeeeeeeee............eeeeeee..hhhhh......hhhhh..hhh.eeeeee....eeee..........ee..ee............ee......eeeeeeeeeeeeeee......eeeeeeeeeeee...eeeeeeeeee.....eeeeeeeeeee....eeeeeeeeeeeee.....eeeeee...hhhhh...eeeeeeeeee..........eeeeeeeeeeeee...........eeeeeee......eeeeeeeeeeeeee..hhhhh..........hhhhhhhhhhhh........eeehhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wcd J  11 IVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQGNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLPGGVYALNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQPGGVTITLFSANIDAITSLSVGGELVFRTSVHGLVLGATIYLIGFDGTTVITRAVAANNGLTTGTDNLMPFNLVIPTNEITQPITSIKLEIVTSKSGGQAGDQMSWSARGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVAD 431
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430
   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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain J   (POLS_IBDVC | P15480)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0039621    T=13 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=13 symmetry. The T=13 capsid is composed of 12 pentameric and 120 hexameric capsomeres.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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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  1wcd
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLS_IBDVC | P15480: 1wce

(-) Related Entries Specified in the PDB File

1wce CRYSTAL STRUCTURE OF THE T13 IBDV VIRAL PARTICLE REVEALS A MISSING LINK IN ICOSAHEDRAL VIRUSES EVOLUTION