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(-) Description

Title :  DIMERIC ROUS SARCOMA VIRUS CAPSID PROTEIN STRUCTURE WITH AN UPSTREAM 25-AMINO ACID RESIDUE EXTENSION OF C-TERMINAL OF GAG P10 PROTEIN
 
Authors :  N. Nandhagopal, A. A. Simpson, M. C. Johnson, A. B. Francisco, G. W. Scha M. G. Rossmann, V. M. Vogt
Date :  02 May 03  (Deposition) - 23 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Retrovirus, Capsid Protein, Gag Polyprotein, Immature Gag, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nandhagopal, A. A. Simpson, M. C. Johnson, A. B. Francisco, G. W. Schatz, M. G. Rossmann, V. M. Vogt
Dimeric Rous Sarcoma Virus Capsid Protein Structure Relevan To Immature Gag Assembly
J. Mol. Biol. V. 335 275 2004
PubMed-ID: 14659756  |  Reference-DOI: 10.1016/J.JMB.2003.10.034

(-) Compounds

Molecule 1 - GAG POLYPROTEIN CAPSID PROTEIN P27
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN
    Organism Scientific: ROUS SARCOMA VIRUS
    Organism Taxid: 11886

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1P7N)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P7N)

(-) Exons   (0, 0)

(no "Exon" information available for 1P7N)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:176
 aligned with GAG_RSVP | P03322 from UniProtKB/Swiss-Prot  Length:701

    Alignment length:192
                                   204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384  
             GAG_RSVP   195 GDTPPGAEQSRAEPGHAGQAPGPALTDWARVREELASTGPPVVAMPVVIKTEGPAWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSSPLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAAATRDPRHPANGQGRGERTNLNRLKGLADGMVGNPQGQAALLRPGELVAITASALQAFREVARLA 386
               SCOP domains d1p7n                a_ A: RSV capsid protein                                                                                                                                                    SCOP domains
               CATH domains 1p7nA                00 A:-28-147 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------Gag_p24-1p7nA01 A:16-147                                                                                                             Pfam domains
         Sec.struct. author .....----------------.....hhhhhhhhhhh......................hhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1p7n A -28 GPTSP----------------GPALTDWARVREELASTGPPVVAMPVVIKTEGPAWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSSPLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAAATRDPRHPANGQGRGERTNLNRLKGLADGMVGNPQGQAALLRPGELVAITASALQAFREVARLA 147
                                |    -         - |     -15        -5         5        15        25        35        45        55        65        75        85        95       105       115       125       135       145  
                              -24              -23
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  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 alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Viral_Gag (25)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (GAG_RSVP | P03322)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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.
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
        GAG_RSVP | P03322: 1a6s 1bai 1em9 1eoq 2ihx 2rsp 2x8q 3g0v 3g1g 3g1i 3g21 3g26 3g28 3g29 5a9e

(-) Related Entries Specified in the PDB File

1em9 THE SAME PROTEIN WITHOUT THE UPSTREAM EXTENSION