› 4h8k

X-ray diffraction
2.3Å resolution

Crystal structure of LC11-RNase H1 in complex with RNA/DNA hybrid

Released:
DOI: 10.2210/pdb4h8k/pdb
PDB entry 4h8k coloured by chain, front view.
PDB entry 4h8k coloured by chain, side view.
PDB entry 4h8k coloured by chain, top view.
Source organism: uncultured organism
Primary publication:
Crystal structure of metagenome-derived LC11-RNase H1 in complex with RNA/DNA hybrid.
Nguyen TN, You DJ, Matsumoto H, Kanaya E, Koga Y, Kanaya S
J Struct Biol 182 144-54 (2013)
PMID: 23500886

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117577 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
RNase H type-1 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 140 amino acids
Theoretical weight: 15.63 KDa
Source organism: uncultured organism
Expression system: Escherichia coli
UniProt:
  • Canonical: E0X767 (Residues: 1-140; Coverage: 100%)
Sequence domains: Reverse transcriptase-like
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 14 nucleotides
Theoretical weight: 4.36 KDa
Source organism: uncultured organism
Expression system: Not provided
RNA (5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.38 KDa
Source organism: uncultured organism
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 42.613Å b: 90.758Å c: 55.605Å
α: 90° β: 97.82° γ: 90°
R-values:
R R work R free
0.21 0.207 0.278
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Trinucleotide expansion in disease: why is there a length threshold?
Lee et al. (2014)
5 other articles

2 mentions without citation

DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues.
Yan et al. (2017)
1 more