› 3o3g

X-ray diffraction
2.1Å resolution

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

Released:
DOI: 10.2210/pdb3o3g/pdb
PDB entry 3o3g coloured by chain, front view.
PDB entry 3o3g coloured by chain, side view.
PDB entry 3o3g 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-113134 (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 CA 5 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: C2
Unit cell:
a: 106.122Å b: 47.347Å c: 79.012Å
α: 90° β: 132.81° γ: 90°
R-values:
R R work R free
0.175 0.171 0.245
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Processing ribonucleotides incorporated during eukaryotic DNA replication.
Williams et al. (2016)
11 more

7 mentions without citation

The Blueprint of a Minimal Cell: MiniBacillus.
Reuß et al. (2016)
6 more