› 4hht

X-ray diffraction
3.1Å resolution

T. maritima RNase H2 G21S in complex with nucleic acid substrate and calcium ions

Released:
DOI: 10.2210/pdb4hht/pdb
PDB entry 4hht coloured by chain, front view.
PDB entry 4hht coloured by chain, side view.
PDB entry 4hht coloured by chain, top view.
Source organism: Thermotoga maritima MSB8
Primary publication:
RNase H2 roles in genome integrity revealed by unlinking its activities.
Chon H, Sparks JL, Rychlik M, Nowotny M, Burgers PM, Crouch RJ, Cerritelli SM
Nucleic Acids Res 41 3130-43 (2013)
PMID: 23355612

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113149 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
Ribonuclease HII Chain: A
Molecule details ›
Chain: A
Length: 237 amino acids
Theoretical weight: 26.57 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X017 (Residues: 2-238; Coverage: 100%)
Gene names: TM_0915, rnhB
Sequence domains: Ribonuclease HII
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Not provided
DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 106.952Å b: 47.626Å c: 77.451Å
α: 90° β: 131.26° γ: 90°
R-values:
R R work R free
0.182 0.178 0.254
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

27 review citations

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression.
Skourti-Stathaki et al. (2014)
26 more

2 mentions without citation

RNase H2 roles in genome integrity revealed by unlinking its activities.
Chon et al. (2013)
1 more