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(-) Description

Title :  STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION BY CRYO-ELECTRON MICROSCOPY
 
Authors :  T. A. M. Bharat, N. E. Davey, P. Ulbrich, J. D. Riches, A. D. Marco, M. Ruml C. Sachse, T. Ruml, J. A. G. Briggs
Date :  23 Apr 12  (Deposition) - 30 May 12  (Release) - 19 Apr 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  7.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Protein, Retrovirus, Gag (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. M. Bharat, N. E. Davey, P. Ulbrich, J. D. Riches, A. D. Marco, M. Rumlova, C. Sachse, T. Ruml, J. A. G. Briggs
Structure Of The Immature Retroviral Capsid At 8A Resolutio By Cryo-Electron Microscopy.
Nature V. 487 385 2012
PubMed-ID: 22722831  |  Reference-DOI: 10.1038/NATURE11169

(-) Compounds

Molecule 1 - CAPSID PROTEIN P27
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: M-PMV CA-NTD, RESIDUES 318-433
    Organism Scientific: MASON-PFIZER MONKEY VIRUS
    Organism Taxid: 11855
    Synonym: M-PMV DPRO CANC PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4ARD)

(-) Sites  (0, 0)

(no "Site" information available for 4ARD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ARD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ARD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ARD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ARD)

(-) Exons   (0, 0)

(no "Exon" information available for 4ARD)

(-) 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:116
 aligned with GAG_MPMV | P07567 from UniProtKB/Swiss-Prot  Length:657

    Alignment length:116
                                   327       337       347       357       367       377       387       397       407       417       427      
             GAG_MPMV   318 FDFAVIKELKTAASQYGATAPYTLAIVESVADNWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAGNGWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRK 433
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4ard A  19 FDFAVIKELKTAASQYGATAPYTLAIVESVADNWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAGNGWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRK 134
                                    28        38        48        58        68        78        88        98       108       118       128      


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with GAG_MPMV | P07567 from UniProtKB/Swiss-Prot  Length:657

    Alignment length:116
                                   327       337       347       357       367       377       387       397       407       417       427      
             GAG_MPMV   318 FDFAVIKELKTAASQYGATAPYTLAIVESVADNWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAGNGWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRK 433
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4ard B  19 FDFAVIKELKTAASQYGATAPYTLAIVESVADNWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAGNGWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRK 134
                                    28        38        48        58        68        78        88        98       108       118       128
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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  (0, 0)

(no "SCOP Domain" information available for 4ARD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ARD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ARD)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GAG_MPMV | P07567)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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_MPMV | P07567: 1bax 1cl4 2kgf 2lpy 2mv4 5ldl 5lmy

(-) Related Entries Specified in the PDB File

1bax MASON-PFIZER MONKEY VIRUS MATRIX PROTEIN, NMR, AVERAGE STRUCTURE
1cl4 NUCLEOCAPSID PROTEIN FROM MASON-PFIZER MONKEY VIRUS (MPMV)
4arg STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION BY CRYO-ELECTRON MICROSCOPY RELATED ID: EMD-2090 RELATED DB: EMDB STRUCTURE OF THE IMMATURE RETROVIRAL CAPSID AT 8A RESOLUTION BY CRYO-ELECTRON MICROSCOPY RELATED ID: EMD-2089 RELATED DB: EMDB