PDBe 3f9k

X-ray diffraction
3.2Å resolution

Two domain fragment of HIV-2 integrase in complex with LEDGF IBD

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)
Endopeptidase for which the P1 residue is preferably hydrophobic.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero nonamer
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Integrase Chains: A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t
Molecule details ›
Chains: A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t
Length: 210 amino acids
Theoretical weight: 23.67 KDa
Source organism: Human immunodeficiency virus type 2 (ISOLATE ROD)
Expression system: Escherichia coli
UniProt:
  • Canonical: P04584 (Residues: 1173-1380; Coverage: 14%)
Gene name: gag-pol
Sequence domains:
Structure domains:
PC4 and SFRS1-interacting protein Chains: C, G, K, O, S, W, a, e, i, m, q, u
Molecule details ›
Chains: C, G, K, O, S, W, a, e, i, m, q, u
Length: 95 amino acids
Theoretical weight: 11.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75475 (Residues: 347-435; Coverage: 17%)
Gene names: DFS70, LEDGF, PSIP1, PSIP2
Structure domains: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 201.36Å b: 202.5Å c: 280.48Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.225 0.234
Expression system: Escherichia coli