› 4ru9

X-ray diffraction
2.65Å resolution

Crystal structure of human DNA polymerase eta inserting dCMPNPP opposite a MeFapy-dG adducted DNA template

Released:
DOI: 10.2210/pdb4ru9/pdb
PDB entry 4ru9 coloured by chain, front view.
PDB entry 4ru9 coloured by chain, side view.
PDB entry 4ru9 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase η and Sulfolobus solfataricus P2 Polymerase IV.
Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M
J Am Chem Soc 137 7011-4 (2015)
PMID: 25988947

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118150 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 432 amino acids
Theoretical weight: 48.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
Structure domains:
Nucleic acids Template: CAT(MF7)ATGACGCT Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: synthetic construct
Expression system: Not provided
Nucleic acids Primar: AGCGTCAT Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand 0KX 1 x 0KX
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P61
Unit cell:
a: 98.971Å b: 98.971Å c: 81.624Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.162 0.159 0.229
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 citation in other articles

Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η.
Genna et al. (2016)
8 more

3 mentions without citation

Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase η and Sulfolobus solfataricus P2 Polymerase IV.
Patra et al. (2015)
2 more