PDBe 2exf

Solution NMR

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

Released:

Function and Biology Details

Reactions catalysed:
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.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (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: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

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