› 2qkk

X-ray diffraction
3.2Å resolution

Human RNase H catalytic domain mutant D210N in complex with 14-mer RNA/DNA hybrid

Released:
DOI: 10.2210/pdb2qkk/pdb
PDB entry 2qkk coloured by chain, front view.
PDB entry 2qkk coloured by chain, side view.
PDB entry 2qkk 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

Assemblies composition:
hetero tetramer (preferred)
hetero trimer
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H1 Chains: A, B, E, F, I, J, M, N, R, S, W
Molecule details ›
Chains: A, B, E, F, I, J, M, N, R, S, W
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*G)-3' Chains: D, H, L, P, U, Z
Molecule details ›
Chains: D, H, L, P, U, Z
Length: 14 nucleotides
Theoretical weight: 4.36 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' Chains: C, G, K, O, T, X
Molecule details ›
Chains: C, G, K, O, T, X
Length: 14 nucleotides
Theoretical weight: 4.38 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand TRS 1 x TRS
Ligand CA 14 x CA
Ligand MES 1 x MES
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 151.065Å b: 176.2Å c: 125.845Å
α: 90° β: 90.22° γ: 90°
R-values:
R R work R free
0.212 0.212 0.268
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

17 mentions without citation

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