› 3o3h

X-ray diffraction
2.8Å resolution

T. maritima RNase H2 D107N in complex with nucleic acid substrate and manganese ions

Released:
DOI: 10.2210/pdb3o3h/pdb
PDB entry 3o3h coloured by chain, front view.
PDB entry 3o3h coloured by chain, side view.
PDB entry 3o3h coloured by chain, top view.
Source organism: Thermotoga maritima
Primary publication:
Crystal structures of RNase H2 in complex with nucleic acid reveal the mechanism of RNA-DNA junction recognition and cleavage.
Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch RJ, Nowotny M
Mol Cell 40 658-70 (2010)
PMID: 21095591

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-113135 (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: 222 amino acids
Theoretical weight: 24.68 KDa
Source organism: Thermotoga maritima
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X017 (Residues: 2-223; Coverage: 93%)
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
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
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 3 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: C2
Unit cell:
a: 104.658Å b: 48.571Å c: 77.91Å
α: 90° β: 131.97° γ: 90°
R-values:
R R work R free
0.189 0.182 0.253
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Intracellular nucleotide levels and the control of retroviral infections.
Amie et al. (2013)
11 more

2 mentions without citation

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