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(-) Description

Title :  ROUS SARCOMA VIRUS CAPSID PROTEIN: N-TERMINAL DOMAIN
 
Authors :  R. L. Kingston, T. Fitzon-Ostendorp, E. Z. Eisenmesser, G. W. Schatz, V. M. Vogt, C. B. Post, M. G. Rossmann
Date :  16 Mar 00  (Deposition) - 02 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Virus/Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. L. Kingston, T. Fitzon-Ostendorp, E. Z. Eisenmesser, G. W. Schatz, V. M. Vogt, C. B. Post, M. G. Rossmann
Structure And Self-Association Of The Rous Sarcoma Virus Capsid Protein.
Structure Fold. Des. V. 8 617 2000
PubMed-ID: 10873863  |  Reference-DOI: 10.1016/S0969-2126(00)00148-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAG POLYPROTEIN CAPSID PROTEIN P27
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN
    Organism ScientificROUS SARCOMA VIRUS - PRAGUE C
    Organism Taxid11888
    StrainPRAGUE C

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , HOH A:302 , HOH A:303 , ASP B:71 , HOH B:304 , HOH B:305BINDING SITE FOR RESIDUE MG A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EM9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EM9)

(-) Exons   (0, 0)

(no "Exon" information available for 1EM9)

(-) 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:147
 aligned with GAG_RSVP | P03322 from UniProtKB/Swiss-Prot  Length:701

    Alignment length:147
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       
             GAG_RSVP   240 PVVIKTEGPAWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSSPLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAAATRDPRHPANGQGRGERTNLNRLKGLADGMVGNPQGQAALLRPGELVAITASALQAFREVARLA 386
               SCOP domains d1em9a_ A: RSV capsid protein                                                                                                                       SCOP domains
               CATH domains 1em9A00 A:1-147 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee...hhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1em9 A   1 PVVIKTEGPAWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSSPLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAAATRDPRHPANGQGRGERTNLNRLKGLADGMVGNPQGQAALLRPGELVAITASALQAFREVARLA 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       

Chain B from PDB  Type:PROTEIN  Length:141
 aligned with GAG_RSVP | P03322 from UniProtKB/Swiss-Prot  Length:701

    Alignment length:147
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       
             GAG_RSVP   240 PVVIKTEGPAWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSSPLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAAATRDPRHPANGQGRGERTNLNRLKGLADGMVGNPQGQAALLRPGELVAITASALQAFREVARLA 386
               SCOP domains d1em9   b_ B: RSV capsid protein                                                                                                                    SCOP domains
               CATH domains 1em9B   00 B:1-147 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..---.ee...hhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........---...hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1em9 B   1 PVVIK---PAWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSSPLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAAATRDPRHPANGQ---ERTNLNRLKGLADGMVGNPQGQAALLRPGELVAITASALQAFREVARLA 147
                                |   10        20        30        40        50        60        70        80        90    |  100       110       120       130       140       
                                5   9                                                                                    95  99                                                

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EM9)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1eoq 1p7n 2ihx 2rsp 2x8q 3g0v 3g1g 3g1i 3g21 3g26 3g28 3g29 5a9e

(-) Related Entries Specified in the PDB File

1eoq C-TERMINAL DOMAIN