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(-) Description

Title :  CRYSTAL STRUCTURE OF JAAGSIEKTE SHEEP RETROVIRUS CAPSID N-TERMINAL DOMAIN
 
Authors :  G. B. Mortuza, D. C. Goldstone, C. Pashley, L. F. Haire, M. Palmarini, W. J. P. Stoye, I. A. Taylor
Date :  30 Sep 08  (Deposition) - 25 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Capsid, Virion, Retrovirus, Zinc-Finger, Metal-Binding, Capsid Protein, Structural Protein, Viral Nucleoprotein, Viral Matrix Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. B. Mortuza, D. C. Goldstone, C. Pashley, L. F. Haire, M. Palmarini, W. R. Taylor, J. P. Stoye, I. A. Taylor
Structure Of The Capsid Amino-Terminal Domain From The Betaretrovirus, Jaagsiekte Sheep Retrovirus.
J. Mol. Biol. V. 386 1179 2009
PubMed-ID: 19007792  |  Reference-DOI: 10.1016/J.JMB.2008.10.066

(-) Compounds

Molecule 1 - CAPSID PROTEIN P27
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: N-TERMINAL DOMAIN, RESIDUES 257-388
    Organism Scientific: JAAGSIEKTE SHEEP RETROVIRUS
    Organism Taxid: 11746
    Synonym: JSRV CAPSID

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V4X)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:131
 aligned with GAG_JSRV | P31622 from UniProtKB/Swiss-Prot  Length:612

    Alignment length:131
                                   266       276       286       296       306       316       326       336       346       356       366       376       386 
             GAG_JSRV   257 PVFENNNQRYYESLPFKQLKELKIACSQYGPTAPFTIAMIESLGTQALPPNDWKQTARACLSGGDYLLWKSEFFEQCARIADVNRQQGIQTSYEMLIGEGPYQATDTQLNFLPGAYAQISNAARQAWKKLP 387
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------Gag_p24-2v4xA01 A:16-131                                                                                             Pfam domains
         Sec.struct. author .eee....eee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhh.....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4x A   1 PVFENNNQRYYESLPFKQLKELKIACSQYGPTAPFTIAmIENLGTQALPPNDWKQTARACLSGGDYLLWKSEFFEQCARIADVNRQQGIQTSYEmLIGEGPYQATDTQLNFLPGAYAQISNAARQAWKRLP 131
                                    10        20        30        40        50        60        70        80        90    |  100       110       120       130 
                                                                 39-MSE                                                  95-MSE
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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  (0, 0)

(no "SCOP Domain" information available for 2V4X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V4X)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Viral_Gag (25)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GAG_JSRV | P31622)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0039660    structural constituent of virion    The action of a molecule that contributes to the structural integrity of a virion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046755    viral budding    A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
    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:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
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: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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