› 3bsu

X-ray diffraction
2.1Å resolution

Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA

Released:
DOI: 10.2210/pdb3bsu/pdb
PDB entry 3bsu coloured by chain, front view.
PDB entry 3bsu coloured by chain, side view.
PDB entry 3bsu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.
Nowotny M, Cerritelli SM, Ghirlando R, Gaidamakov SA, Crouch RJ, Yang W
EMBO J 27 1172-81 (2008)
PMID: 18337749

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116107 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H1 Chains: A, B, C, F, G, H
Molecule details ›
Chains: A, B, C, F, G, H
Length: 53 amino acids
Theoretical weight: 6.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60930 (Residues: 24-76; Coverage: 19%)
Gene names: RNASEH1, RNH1
Sequence domains: Caulimovirus viroplasmin
Structure domains: Ribonuclease H1, N-terminal domain
DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3') Chains: E, J
Molecule details ›
Chains: E, J
Length: 12 nucleotides
Theoretical weight: 3.81 KDa
Source organism: Homo sapiens
Expression system: Not provided
RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3') Chains: D, I
Molecule details ›
Chains: D, I
Length: 12 nucleotides
Theoretical weight: 3.77 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
1 modified residue:
Ligand 5IU 2 x 5IU

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 45.492Å b: 64.262Å c: 140.322Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.29
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Ribonuclease H: the enzymes in eukaryotes.
Cerritelli et al. (2009)
12 more

8 mentions without citation

Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1.
Nguyen et al. (2017)
7 more