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(-) Description

Title :  NMR STRUCTURE OF THE HIV-2 NUCLEOCAPSID PROTEIN
 
Authors :  T. Matsui, Y. Kodera, H. Endoh, E. Miyauchi, H. Komatsu, K. Sato, T. Tanaka, T. Kohno, T. Maeda
Date :  27 Mar 06  (Deposition) - 13 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (13x)
Keywords :  Nucleocapsid Protein, Hiv-2, Rna Recognition, Zinc Finger, Mutant, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Matsui, Y. Kodera, H. Endoh, E. Miyauchi, H. Komatsu, K. Sato, T. Tanaka, T. Kohno, T. Maeda
Rna Recognition Mechanism Of The Minimal Active Domain Of The Human Immunodeficiency Virus Type-2 Nucleocapsid Protein
J. Biochem. (Tokyo) V. 141 269 2007
PubMed-ID: 17202191  |  Reference-DOI: 10.1093/JB/MVM037
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN P7
    Chains: A
    Engineered: YES
    Fragment: RESIDUS 1-29
    Mutation: YES
    Other Details: THIS PEPTIDE HAS BEEN CHEMICALLY SYNTHESIZED
    Synonym: HIV-2 NUCLEOCAPSID PROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (13x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:9 , CYS A:12 , HIS A:17 , CYS A:22BINDING SITE FOR RESIDUE ZN A 30

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:9 -A:22
2A:12 -A:22

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DI2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DI2)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_CCHCPS50158 Zinc finger CCHC-type profile.GAG_HV2G1391-406
413-428		  1A:8-23
-

(-) Exons   (0, 0)

(no "Exon" information available for 2DI2)

(-) Sequences/Alignments

NMR Structure
   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:29
 aligned with GAG_HV2G1 | P18041 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:29
                                   393       403         
            GAG_HV2G1   384 AQQRKVIRCWNCGKEGHSARQCRAPRRQG 412
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .................hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE -------ZF_CCHC         ------ PROSITE
                 Transcript ----------------------------- Transcript
                 2di2 A   1 AQQRKVIRCWACGKEGHSARQCRAPRRQG  29
                                    10        20
   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  (0, 0)

(no "SCOP Domain" information available for 2DI2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DI2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DI2)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (GAG_HV2G1 | P18041)
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        GAG_HV2G1 | P18041: 1nc8 2ec7

(-) Related Entries Specified in the PDB File

1nc8 WILD TYPE SEQUENCE OF THE SAME PEPTIDE