PDBe 2l4l

Solution NMR

Structural insights into the cTAR DNA recognition by the HIV-1 Nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC

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:
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: 45 amino acids
Theoretical weight: 5.15 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 388-432; Coverage: 3%)
Gene name: gag-pol
Sequence domains: Zinc knuckle
Structure domains: Zinc finger, CCHC-type
5'-D(*CP*TP*GP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 4 nucleotides
Theoretical weight: 1.21 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: DGSA-distance geometry simulated annealing
Expression systems:
  • Escherichia coli
  • Not provided