› 3d0p

X-ray diffraction
1.8Å resolution

Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex

Released:
DOI: 10.2210/pdb3d0p/pdb
PDB entry 3d0p coloured by chain, front view.
PDB entry 3d0p coloured by chain, side view.
PDB entry 3d0p coloured by chain, top view.
Source organism: Halalkalibacterium halodurans C-125
Primary publication:
Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex.
Pallan PS, Egli M
Cell Cycle 7 2562-9 (2008)
PMID: 18719385

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116166 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Ribonuclease H Chains: A, C
Molecule details ›
Chains: A, C
Length: 134 amino acids
Theoretical weight: 15.43 KDa
Source organism: Alkalihalobacillus halodurans C-125
Expression system: Not provided
UniProt:
  • Canonical: Q9KEI9 (Residues: 61-194; Coverage: 68%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3') Chains: B, D
Molecule details ›
Chains: B, D
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Halalkalibacterium halodurans C-125
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2
Unit cell:
a: 98.397Å b: 66.66Å c: 76.926Å
α: 90° β: 122.31° γ: 90°
R-values:
R R work R free
0.215 0.214 0.241
Expression system: Not provided

Quick links

Citations

4 review citations

Recent Advances in Oligonucleotide Therapeutics in Oncology.
Xiong et al. (2021)
3 more

5 mentions without citation

Chemistry, structure and function of approved oligonucleotide therapeutics.
Egli et al. (2023)
4 more