› 2exf

Solution NMR

Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site

Released:
DOI: 10.2210/pdb2exf/pdb
PDB entry 2exf coloured by chain, ensemble of 10 models, front view.
PDB entry 2exf coloured by chain, ensemble of 10 models, side view.
PDB entry 2exf coloured by chain, ensemble of 10 models, top view.
Source organisms:
Primary publication:
How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription.
Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF, Roques BP, Mély Y, Bouaziz S, Morellet N
J Mol Biol 383 1112-28 (2008)
PMID: 18773912

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115226 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Nucleocapsid protein p7 Chain: A
Molecule details ›
Chain: A
Length: 44 amino acids
Theoretical weight: 5.02 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P03366 (Residues: 390-432; Coverage: 3%)
Gene name: gag-pol
Sequence domains: Zinc knuckle
Structure domains: Zinc finger, CCHC-type
5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: restrained molecular dynamics restrained simulated annealing energy minimization
Expression system: Not provided

Quick links

Citations

14 review citations

Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription.
Levin et al. (2010)
13 more

6 mentions without citation

Sensing peptide-oligonucleotide interactions by a two-color fluorescence label: application to the HIV-1 nucleocapsid protein.
Shvadchak et al. (2009)
5 more