› 9cj9

X-ray diffraction
2.98Å resolution

Crystal structure of human polymerase eta with incoming dAMPnPP nucleotide opposite O4-methyl threofuranosyl thymidine in DNA template at insertion stage

Released:
DOI: 10.2210/pdb9cj9/pdb
PDB entry 9cj9 coloured by chain, front view.
PDB entry 9cj9 coloured by chain, side view.
PDB entry 9cj9 coloured by chain, top view.
Source organisms:
Primary publication:
DNA Replication across α-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase η.
Tomar R, Ghodke PP, Patra A, Smyth E, Pontarelli A, Copp W, Guengerich FP, Chaput JJ, Wilds CJ, Stone MP, Egli M
Biochemistry (2024)
PMID: 39259676

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-513559 (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: 48.62 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:
DNA (5'-D(*CP*AP*TP*(TFT)P*AP*TP*GP*AP*CP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-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

2 bound ligands:
Ligand DZ4 1 x DZ4
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: P61
Unit cell:
a: 98.08Å b: 98.08Å c: 78.66Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.22 0.348
Expression systems:
  • Escherichia coli
  • Not provided

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