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(-) Description

Title :  1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES
 
Authors :  H. Demene, N. Morellet, V. Teilleux, T. Huynh-Dinh, H. De Rocquigny, M. C. Fournie-Zaluski, B. P. Roques
Date :  03 Jul 98  (Deposition) - 02 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,D  (10x)
Keywords :  Complex (Nucleocapsid Protein/Dna), Nucleic Acid, Retrovirus, Virus Morphogenesis, Zinc Finger, Viral Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Morellet, H. Demene, V. Teilleux, T. Huynh-Dinh, H. De Rocquigny, M. C. Fournie-Zaluski, B. P. Roques
Structure Of The Complex Between The Hiv-1 Nucleocapsid Protein Ncp7 And The Single-Stranded Pentanucleotide D(Acgcc).
J. Mol. Biol. V. 283 419 1998
PubMed-ID: 9769215  |  Reference-DOI: 10.1006/JMBI.1998.2098
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*CP*GP*CP*C)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - NUCLEOCAPSID PROTEIN 7
    Chains: A
    Engineered: YES
    Fragment: RESIDUES 12-53
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: MAL
    Synonym: (12-53)NCP7

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:15 , CYS A:18 , HIS A:23 , CYS A:28BINDING SITE FOR RESIDUE ZN A 54H
2AC2SOFTWARECYS A:36 , CYS A:39 , HIS A:44 , CYS A:49BINDING SITE FOR RESIDUE ZN A 55H
3ZNBUNKNOWNCYS A:15 , CYS A:18 , HIS A:23 , CYS A:28 , CYS A:36 , CYS A:39 , HIS A:44ZINC-BINDING SITES.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BJ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BJ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BJ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BJ6)

(-) Exons   (0, 0)

(no "Exon" information available for 1BJ6)

(-) 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:42
 aligned with Q74084_9HIV1 | Q74084 from UniProtKB/TrEMBL  Length:512

    Alignment length:46
                                   394       404       414       424      
         Q74084_9HIV1   385 NQRKMVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ 430
               SCOP domains d    1bj6a_ A: HIV nucleocapsid                SCOP domains
               CATH domains 1    bj6A00 A:12-53 HIV-1 Nucleocapsid Protein CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .----......................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1bj6 A  12 N----VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ  53
                            |    |  17        27        37        47      
                            |   13                                        
                           12                                             


Chain D from PDB  Type:DNA  Length:5
                                     
                 1bj6 D   1 ACGCC   5
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BJ6)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (Q74084_9HIV1 | Q74084)
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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