› 4fo6

X-ray diffraction
2.01Å resolution

Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and an rCMP at the primer terminus.

Released:
DOI: 10.2210/pdb4fo6/pdb
PDB entry 4fo6 coloured by chain, front view.
PDB entry 4fo6 coloured by chain, side view.
PDB entry 4fo6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The catalytic cycle for ribonucleotide incorporation by human DNA Pol λ.
Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek K
Nucleic Acids Res 40 7518-27 (2012)
PMID: 22584622

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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113147 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
1 distinct DNA/RNA hybrid molecule
Macromolecules (6 distinct):
DNA polymerase lambda Chain: A
Molecule details ›
Chain: A
Length: 329 amino acids
Theoretical weight: 36.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGP5 (Residues: 242-575; Coverage: 57%)
Gene name: POLL
Sequence domains:
Structure domains:
5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3' Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(P*GP*CP*CP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(P*TP*AP*CP*TP*G)-3' Chain: H
Molecule details ›
Chain: H
Length: 5 nucleotides
Theoretical weight: 1.5 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(P*CP*AP*GP*TP*A)-3' Chain: I
Molecule details ›
Chain: I
Length: 5 nucleotides
Theoretical weight: 1.5 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*AP*GP*TP*AP)-R(P*C)-3' Chain: P
Molecule details ›
Chain: P
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand MG 1 x MG
Ligand NA 2 x NA
Ligand CL 1 x CL
Ligand MN 1 x MN
Ligand F2A 1 x F2A
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 55.78Å b: 63.655Å c: 141.47Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.231
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Ribonucleotides in DNA: origins, repair and consequences.
Williams et al. (2014)
7 more

2 mentions without citation

Structure-function studies of DNA polymerase λ.
Bebenek et al. (2014)
1 more