› 6d0z

X-ray diffraction
1.75Å resolution

Polymerase Eta cytarabine (AraC) extension ternary complex

Released:
DOI: 10.2210/pdb6d0z/pdb
PDB entry 6d0z coloured by chain, front view.
PDB entry 6d0z coloured by chain, side view.
PDB entry 6d0z coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for polymerase η-promoted resistance to the anticancer nucleoside analog cytarabine.
Rechkoblit O, Choudhury JR, Buku A, Prakash L, Prakash S, Aggarwal AK
Sci Rep 8 12702 (2018)
PMID: 30140014

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-119715 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 48.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
Structure domains:
DNA (5'-D(*CP*AP*TP*TP*GP*CP*AP*GP*TP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA/RNA (5'-D(*AP*GP*CP*AP*CP*TP*G)-R(P*(CAR))-3') 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

3 bound ligands:
Ligand MG 2 x MG
Ligand DZ4 1 x DZ4
Ligand GOL 2 x GOL
1 modified residue:
Ligand CAR 1 x CAR

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P61
Unit cell:
a: 98.789Å b: 98.789Å c: 81.772Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.17 0.168 0.195
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

1 review citation

Multifaceted activities of DNA polymerase η: beyond translesion DNA synthesis.
Acharya et al. (2019)
4 other articles

2 mentions without citation

Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η.
Rechkoblit et al. (2019)
1 more