› 2qk9

X-ray diffraction
2.55Å resolution

Human RNase H catalytic domain mutant D210N in complex with 18-mer RNA/DNA hybrid

Released:
DOI: 10.2210/pdb2qk9/pdb
PDB entry 2qk9 coloured by chain, front view.
PDB entry 2qk9 coloured by chain, side view.
PDB entry 2qk9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription.
Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W
Mol Cell 28 264-76 (2007)
PMID: 17964265

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115802 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H1 Chain: A
Molecule details ›
Chain: A
Length: 154 amino acids
Theoretical weight: 17.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O60930 (Residues: 136-286; Coverage: 53%)
Gene names: RNASEH1, RNH1
Sequence domains: RNase H
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-R(*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 18 nucleotides
Theoretical weight: 5.71 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand SO4 7 x SO4
Ligand 16D 1 x 16D
Ligand NA 1 x NA
Ligand FLC 1 x FLC
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: R32
Unit cell:
a: 158.578Å b: 158.578Å c: 142.055Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.19 0.19 0.216
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

27 review citations

Ribonuclease H: the enzymes in eukaryotes.
Cerritelli et al. (2009)
26 more

22 mentions without citation

Enzyme dynamics from NMR spectroscopy.
Palmer AG. (2015)
21 more