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(-) Description

Title :  PORCINE PARVOVIRUS CAPSID
 
Authors :  A. A. Simpson, B. Hebert, G. M. Sullivan, C. R. Parrish, Z. Zadori, P. Tijssen, M. G. Rossmann
Date :  04 Oct 01  (Deposition) - 24 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  Capsid, Icosahadral, Beta Sheet, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Simpson, B. Hebert, G. M. Sullivan, C. R. Parrish, Z. Zadori, P. Tijssen, M. G. Rossmann
The Structure Of Porcine Parvovirus: Comparison With Related Viruses.
J. Mol. Biol. V. 315 1189 2002
PubMed-ID: 11827486  |  Reference-DOI: 10.1006/JMBI.2001.5319
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP2
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7108
    Expression System Vector: PFASTBAC
    Expression System Vector Type: BACULOVIRUS
    Gene: VP2
    Organism Scientific: PORCINE PARVOVIRUS
    Organism Taxid: 10796
    Synonym: COAT PROTEIN VP2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1K3V)

(-) Sites  (0, 0)

(no "Site" information available for 1K3V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K3V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:219 -Pro A:220
2Phe A:460 -Pro A:461

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K3V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K3V)

(-) Exons   (0, 0)

(no "Exon" information available for 1K3V)

(-) 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:542
 aligned with CAPSD_PAVPN | P18546 from UniProtKB/Swiss-Prot  Length:729

    Alignment length:542
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727  
          CAPSD_PAVPN   188 GVGVSTGTFNNQTEFQYLGEGLVRITAHASRLIHLNMPEHETYKRIHVLNSESGVAGQMVQDDAHTQMVTPWSLIDANAWGVWFNPADWQLISNNMTEINLVSFEQEIFNVVLKTITESATSPPTKIYNNDLTASLMVALDTNNTLPYTPAAPRSETLGFYPWLPTKPTQYRYYLSCIRNLNPPTYTGQSQQITDSIQTGLHSDIMFYTIENAVPIHLLRTGDEFSTGIYHFDTKPLKLTHSWQTNRSLGLPPKLLTEPTTEGDQHPGTLPAANTRKGYHQTINNSYTEATAIRPAQVGYNTPYMNFEYSNGGPFLTPIVPTADTQYNDDEPNGAIRFTMDYQHGHLTTSSQELERYTFNPQSKCGRAPKQQFNQQAPLNLENTNNGTLLPSDPIGGKSNMHFMNTLNTYGPLTALNNTAPVFPNGQIWDKELDTDLKPRLHVTAPFVCKNNPPGQLFVKIAPNLTDDFNADSPQQPRIITYSNFWWKGTLTFTAKMRSSNMWNPIQQHTTTAENIGNYIPTNIGGIRMFPEYSQLIPRKLY 729
               SCOP domains d1k3va_ A: Parvovirus (panleukopenia virus) capsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1k3vA00 A:38-579 Empty Capsid Viral Protein 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee...eeeeeeeeeeeeeee.......eeeee.hhhhhh.hhhhhh..eeeeeeeeee....hhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeeeeeeee.....eeeeee.....eeeeee.........hhhhh.............eeeeee..........................hhhhh...hhhhhh.eeee.....ee...ee.....ee.ee...hhhhh...............................................ee........eeee..eeee.............hhhhh.ee....................ee..............ee............ee............hhhhh.......ee.............ee................ee.......eeeeee...................eeeeeeeeeeeeeeeee.................hhhhhh................ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k3v A  38 GVGVSTGTFNNQTEFQYLGEGLVRITAHASRLIHLNMPEHETYKRIHVLNSESGVAGQMVQDDAHTQMVTPWSLIDANAWGVWFNPADWQLISNNMTEINLVSFEQEIFNVVLKTITESATSPPTKIYNNDLTASLMVALDTNNTLPYTPAAPRSETLGFYPWLPTKPTQYRYYLSCIRNLNPPTYTGQSQQITDSIQTGLHSDIMFYTIENAVPIHLLRTGDEFSTGIYHFDTKPLKLTHSWQTNRSLGLPPKLLTEPTTEGDQHPGTLPAANTRKGYHQTINNSYTEATAIRPAQVGYNTPYMNFEYSNGGPFLTPIVPTADTQYNDDEPNGAIRFTMDYQHGHLTTSSQELERYTFNPQSKCGRAPKQQFNQQAPLNLENTNNGTLLPSDPIGGKSNMHFMNTLNTYGPLTALNNTAPVFPNGQIWDKELDTDLKPRLHVTAPFVCKNNPPGQLFVKIAPNLTDDFNADSPQQPRIITYSNFWWKGTLTFTAKMRSSNMWNPIQQHTTTAENIGNYIPTNIGGIRMFPEYSQLIPRKLY 579
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1K3V)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (CAPSD_PAVPN | P18546)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0075521    microtubule-dependent intracellular transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus using host microtubules.
    GO:0039665    permeabilization of host organelle membrane involved in viral entry into host cell    Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
    GO:0075606    transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus. The process begins after viral entry, and ends when the viral material is at the nuclear membrane.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0039615    T=1 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=1 symmetry. The T=1 capsid is composed of 12 pentameric capsomeres.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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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  Cis Peptide Bonds
    Asn A:219 - Pro A:220   [ RasMol ]  
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1dnv GALLERIA MELLONELLA DENSONUCLEOSIS VIRUS
1fpv FELINE PANLEUKOPENIA VIRUS
1mvm MINUTE VIRUS OF MICE
4dpv CANINE PARVOVIRUS