› 2qkb

X-ray diffraction
2.4Å resolution

Human RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid

Released:
DOI: 10.2210/pdb2qkb/pdb
PDB entry 2qkb coloured by chain, front view.
PDB entry 2qkb coloured by chain, side view.
PDB entry 2qkb 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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115803 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 154 amino acids
Theoretical weight: 17.29 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(*DGP*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*DTP*DGP*DTP*DCP*DGP*DCP*DAP*DCP*DTP*DCP*DT)-3' Chain: D
Molecule details ›
Chain: D
Length: 20 nucleotides
Theoretical weight: 6.15 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-R(*GP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 20 nucleotides
Theoretical weight: 6.38 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand EDO 2 x EDO
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P3221
Unit cell:
a: 109.991Å b: 109.991Å c: 67.253Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.208 0.208 0.255
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

28 review citations

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

10 mentions without citation

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)
9 more