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(-) Description

Title :  STRUCTURE OF THE (13-51) DOMAIN OF THE NUCLEOCAPSID PROTEIN NCP8 FROM SIVLHOEST
 
Authors :  N. Morellet, H. Meudal, S. Bouaziz, B. P. Roques
Date :  30 Jun 05  (Deposition) - 20 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sivlhoest, Nmr Structure, Ncp8, Nucleocapsid, Viral Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Morellet, H. Meudal, S. Bouaziz, B. P. Roques
Structure Of The Zinc Finger Domain Encompassing Residues 13-51 Of The Nucleocapsid Protein From Simian Immunodeficiency Virus
Biochem. J. V. 393 725 2006
PubMed-ID: 16229684  |  Reference-DOI: 10.1042/BJ20051203
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: A
    Engineered: YES
    Fragment: ZINC FINGER DOMAIN
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN SIV(SIMIAN IMMUNODEFICIENCY VIRUS)
    Synonym: NUCLEOCAPSID PROTEIN NCP8
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:3 , CYS A:6 , HIS A:11 , CYS A:16 , GLN A:18BINDING SITE FOR RESIDUE ZN A 54H
2AC2SOFTWARECYS A:24 , CYS A:27 , HIS A:32 , CYS A:37BINDING SITE FOR RESIDUE ZN A 55H

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A51)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A51)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A51)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A51)

(-) Exons   (0, 0)

(no "Exon" information available for 2A51)

(-) 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:39
 aligned with Q9Q0A3_SIV | Q9Q0A3 from UniProtKB/TrEMBL  Length:512

    Alignment length:39
                                   400       410       420         
           Q9Q0A3_SIV   391 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK 429
               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
                 2a51 A   1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK  39
                                    10        20        30
   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 2A51)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A51)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A51)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (Q9Q0A3_SIV | Q9Q0A3)
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: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: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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