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(-) Description

Title :  STRUCTURE OF THE N-TERMINAL CAPSID DOMAIN OF HIV-2
 
Authors :  A. J. Price, F. Marzetta, M. Lammers, L. M. J. Ylinen, T. Schaller, S. J. W G. J. Towers, L. C. James
Date :  26 Jun 09  (Deposition) - 22 Sep 09  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Protein, Rna-Binding, Capsid Protein, Viral Nucleoprotein, Hiv, Aids, Hiv-2, Hiv-1 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Price, F. Marzetta, M. Lammers, L. M. J. Ylinen, T. Schaller, S. J. Wilson, G. J. Towers, L. C. James
Active Site Remodelling Switches Hiv Specificity Of Antiretroviral Trimcyp
Nat. Struct. Mol. Biol. V. 16 1036 2009
PubMed-ID: 19767750  |  Reference-DOI: 10.1038/NSMB.1667

(-) Compounds

Molecule 1 - GAG POLYPROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN, RESIDUES 99-242
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE D194)
    Organism Taxid11713
    SynonymHIV-2 CAPSID,
 
Molecule 2 - GAG POLYPROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN, RESIDUES 99-242
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE D194)
    Organism Taxid11713
    SynonymHIV-2 CAPSID,

 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 2WLV)

(-) Sites  (0, 0)

(no "Site" information available for 2WLV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:87 -Pro A:88
2Gly B:87 -Pro B:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WLV)

(-) 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:144
 aligned with GAG_HV2RO | P04590 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:144
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275    
            GAG_HV2RO   136 PVQHVGGNYTHIPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAAEWDVQHPIPGPLPAGQLREPRGSDIAGTTSTVEEQIQWMFRPQNPVPVGNIYRRWIQIGLQKCVRMY 279
               SCOP domains d2wlva_ A: automated matches                                                                                                                     SCOP domains
               CATH domains 2wlvA00 A:1-144 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wlv A   1 PVQHVGGTYTHIPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAAEWDVQHPIPGPLPAGQLREPRGSDIAGTTSTVEEQIQWMFRPQNPVPVGNIYRRWIQIGLQKCVRMY 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    

Chain A from PDB  Type:PROTEIN  Length:144
 aligned with Q76929_9HIV2 | Q76929 from UniProtKB/TrEMBL  Length:260

    Alignment length:144
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238    
         Q76929_9HIV2    99 PVQHVGGNYTHIPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAAEWDVQHPIPGPLPAGQLREPRGSDIAGTTSTVDEQIQWMFRPQNPVPVGNIYRRWIQIGLQKCVRMY 242
               SCOP domains d2wlva_ A: automated matches                                                                                                                     SCOP domains
               CATH domains 2wlvA00 A:1-144 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wlv A   1 PVQHVGGTYTHIPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAAEWDVQHPIPGPLPAGQLREPRGSDIAGTTSTVEEQIQWMFRPQNPVPVGNIYRRWIQIGLQKCVRMY 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with GAG_HV2RO | P04590 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:144
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275    
            GAG_HV2RO   136 PVQHVGGNYTHIPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAAEWDVQHPIPGPLPAGQLREPRGSDIAGTTSTVEEQIQWMFRPQNPVPVGNIYRRWIQIGLQKCVRMY 279
               SCOP domains d2wlvb_ B: automated matches                                                                                                                     SCOP domains
               CATH domains 2wlvB00 B:1-144 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                               CATH domains
           Pfam domains (1) Gag_p17-2------Gag_p24-2wlvB03 B:16-144                                                                                                          Pfam domains (1)
           Pfam domains (2) Gag_p17-2------Gag_p24-2wlvB04 B:16-144                                                                                                          Pfam domains (2)
         Sec.struct. author .eee....eee...hhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wlv B   1 PVQHVGGTYTHIPLSPRTLNAWVKLVQQKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAAEWDVQHPIPGPLPAGQLREPRGSDIAGTTSTVEEQIQWMFRPQNPVPVGNIYRRWIQIGLQKCVRMY 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with Q76929_9HIV2 | Q76929 from UniProtKB/TrEMBL  Length:260

    Alignment length:144
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238    
         Q76929_9HIV2    99 PVQHVGGNYTHIPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAAEWDVQHPIPGPLPAGQLREPRGSDIAGTTSTVDEQIQWMFRPQNPVPVGNIYRRWIQIGLQKCVRMY 242
               SCOP domains d2wlvb_ B: automated matches                                                                                                                     SCOP domains
               CATH domains 2wlvB00 B:1-144 Human Immunodeficiency Virus Type 1 Capsid Protein                                                                               CATH domains
           Pfam domains (1) Gag_p17-2------Gag_p24-2wlvB03 B:16-144                                                                                                          Pfam domains (1)
           Pfam domains (2) Gag_p17-2------Gag_p24-2wlvB04 B:16-144                                                                                                          Pfam domains (2)
         Sec.struct. author .eee....eee...hhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wlv B   1 PVQHVGGTYTHIPLSPRTLNAWVKLVQQKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAAEWDVQHPIPGPLPAGQLREPRGSDIAGTTSTVEEQIQWMFRPQNPVPVGNIYRRWIQIGLQKCVRMY 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    

   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/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Matrix (11)

(-) Gene Ontology  (21, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q76929_9HIV2 | Q76929)
molecular function
    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.
biological 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.
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.

Chain A,B   (GAG_HV2RO | P04590)
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: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: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: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: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:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. 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.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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    Gly A:87 - Pro A:88   [ RasMol ]  
    Gly B:87 - Pro B:88   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        GAG_HV2RO | P045904dgb

(-) Related Entries Specified in the PDB File

2wlw STRUCTURE OF THE N-TERMINAL CAPSID DOMAIN OF HIV-2