PDBe 1f6u

Solution NMR

NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. Implications for genome recognition

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
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Nucleocapsid protein p7 Chain: A
Molecule details ›
Chain: A
Length: 56 amino acids
Theoretical weight: 6.38 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P35963 (Residues: 378-432; Coverage: 4%)
Gene name: gag-pol
Sequence domains: Zinc knuckle
Structure domains: HIV-1 Nucleocapsid Protein
HIV-1 STEM-LOOP SL2 FROM PSI-RNA PACKAGING Chain: B
Molecule details ›
Chain: B
Length: 19 nucleotides
Theoretical weight: 6.16 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 75%
Refinement method: distance geometry, simulated annealing
Chemical shifts: BMR4781   BMR4780  
Expression systems:
  • Escherichia coli
  • Not provided