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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE ROUS SARCOMA VIRUS CAPSID PROTEIN: MUTANT D179N, LOW PH
 
Authors :  R. L. Kingston
Date :  30 Jan 09  (Deposition) - 02 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha-Helical Bundle, Capsid Protein, Virion, Viral Protein, Retrovirus (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. D. Bailey, J. K. Hyun, A. K. Mitra, R. L. Kingston
Proton-Linked Dimerization Of A Retroviral Capsid Protein Initiates Capsid Assembly
Structure V. 17 737 2009
PubMed-ID: 19446529  |  Reference-DOI: 10.1016/J.STR.2009.03.010

(-) Compounds

Molecule 1 - GAG POLYPROTEIN
    ChainsA
    EC Number3.4.23.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTYB11
    Expression System StrainROSETTA 2 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN, UNP RESIDUES 389-465
    GeneGAG
    MutationYES
    Organism CommonRSV-PRC
    Organism ScientificROUS SARCOMA VIRUS
    Organism Taxid11888
    StrainPRAGUE C STRAIN
    SynonymCAPSID PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NO32Ligand/IonNITRATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NO34Ligand/IonNITRATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:32 , ASP A:200 , ILE A:201 , LEU A:204 , GLY A:216 , GLU A:217 , LYS A:220 , GLN A:226BINDING SITE FOR RESIDUE NO3 A 1
2AC2SOFTWAREHOH A:25 , TRP A:153 , ASN A:179 , ASP A:191 , ARG A:194 , GLN A:195BINDING SITE FOR RESIDUE NO3 A 227
3AC3SOFTWAREHOH A:3 , HOH A:12 , HOH A:14 , HOH A:31 , HOH A:37 , HOH A:48 , LYS A:173 , GLN A:203 , TYR A:221 , ASP A:224 , ARG A:225BINDING SITE FOR RESIDUE GOL A 3968

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G28)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G28)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G28)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G28)

(-) Exons   (0, 0)

(no "Exon" information available for 3G28)

(-) 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:77
 aligned with GAG_RSVP | P03322 from UniProtKB/Swiss-Prot  Length:701

    Alignment length:77
                                   398       408       418       428       438       448       458       
             GAG_RSVP   389 AGPWADIMQGPSESFVDFANRLIKAVEGSDLPPSARAPVIIDCFRQKSQPDIQQLIRTAPSTLTTPGEIIKYVLDRQ 465
               SCOP domains d3g28a_ A: automated matches                                                  SCOP domains
               CATH domains 3g28A00 A:150-226  [code=1.10.1200.30, no name defined]                       CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 3g28 A 150 AGPWADIMQGPSESFVDFANRLIKAVEGSNLPPSARAPVIIDCFRQKSQPDIQQLIRTAPSTLTTPGEIIKYVLDRQ 226
                                   159       169       179       189       199       209       219       

   Legend:   → Mismatch (orange background)
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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

(-) CATH Domains  (1, 1)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G28)

(-) 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 | P033221a6s 1bai 1em9 1eoq 1p7n 2ihx 2rsp 2x8q 3g0v 3g1g 3g1i 3g21 3g26 3g29 5a9e

(-) Related Entries Specified in the PDB File

3g0v 3g1g 3g1i 3g21 3g26 3g29