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(-) Description

Title :  STRUCTURE OF THE AMINO-TERMINAL CAPSID RESTRICTION ESCAPE MUTATION N-MLV L10W
 
Authors :  D. C. Goldstone, K. Holden-Dye, S. Ohkura, J. P. Stoye, I. A. Taylor
Date :  11 Jan 11  (Deposition) - 23 Nov 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Viral Protein, Restriction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ohkura, D. C. Goldstone, M. W. Yap, K. Holden-Dye, I. A. Taylor, J. P. Stoye
Novel Escape Mutants Suggest An Extensive Trim5Alpha Binding Site Spanning The Entire Outer Surface Of The Murine Leukemia Virus Capsid Protein.
Plos Pathog. V. 7 2011 2011
PubMed-ID: 21483490  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002011

(-) Compounds

Molecule 1 - CAPSID PROTEIN P30
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET22B
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, RESIDUES 215-346
    Mutation: YES
    Organism Scientific: MURINE LEUKEMIA VIRUS
    Organism Taxid: 11786
    Synonym: CA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:12 , THR A:51 , ASP A:53 , ASP A:103 , ASP A:105 , HOH A:2043 , HOH A:2097 , HOH A:2099BINDING SITE FOR RESIDUE GOL A1136

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y4Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y4Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y4Z)

(-) Sequences/Alignments

Asymmetric/Biological 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:135
 aligned with GAG_MLVAV | P03336 from UniProtKB/Swiss-Prot  Length:537

    Alignment length:156
                                   224       234       244       254       264       274       284       294       304       314       324       334       344       354       364      
            GAG_MLVAV   215 PLRLGGNGQLQYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLTTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLPNEVDAAFPLERPDWDYTTQRGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLER 370
               SCOP domains d2y4za_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author eeee.....eeee..hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh---------------------hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y4z A   1 PLRLGGNGQWQYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLTTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLPNEVDAAFPLERPDWDYTTQRGRNHLVLYRQLLLAGLQNAGRS---------------------LEH 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 |       -         -   |  
                                                                                                                                                             132                   133
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y4Z)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GAG_MLVAV | P03336)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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.
    GO:0019068    virion assembly    A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044185    host cell late endosome membrane    The lipid bilayer surrounding a host cell late endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0072494    host multivesicular body    A late endosome in which regions of the limiting host cell endosomal membrane invaginate to form internal vesicles; host membrane proteins that enter the internal vesicles are sequestered from the host cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        GAG_MLVAV | P03336: 1u7k 3bp9

(-) Related Entries Specified in the PDB File

1u7k STRUCTURE OF A HEXAMERIC N-TERMINAL DOMAIN FROM MURINELEUKEMIA VIRUS CAPSID