› 7m0e

X-ray diffraction
2.25Å resolution

Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and incoming dUMPNPP

Released:
DOI: 10.2210/pdb7m0e/pdb
PDB entry 7m0e coloured by chain, front view.
PDB entry 7m0e coloured by chain, side view.
PDB entry 7m0e coloured by chain, top view.
Source organisms:
Primary publication:
Analysis of diverse double-strand break synapsis with Polλ reveals basis for unique substrate specificity in nonhomologous end-joining.
Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC
Nat Commun 13 3806 (2022)
PMID: 35778389

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121573 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 348 amino acids
Theoretical weight: 38.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGP5 (Residues: 232-575; Coverage: 60%)
Gene name: POLL
Sequence domains:
DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3') Chains: G, K, O, T
Molecule details ›
Chains: G, K, O, T
Length: 7 nucleotides
Theoretical weight: 2.12 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') Chains: F, J, N, R
Molecule details ›
Chains: F, J, N, R
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*CP*CP*G)-3') Chains: H, L, P, U
Molecule details ›
Chains: H, L, P, U
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand DUP 4 x DUP
Ligand MG 6 x MG
Ligand NA 4 x NA
Ligand EDO 2 x EDO
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 64.966Å b: 85.819Å c: 91.421Å
α: 105.224° β: 92.576° γ: 111.296°
R-values:
R R work R free
0.185 0.184 0.222
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 citation in other articles

Polλ promotes microhomology-mediated end-joining.
Chandramouly et al. (2023)
3 more

1 mention without citation

Analysis of diverse double-strand break synapsis with Polλ reveals basis for unique substrate specificity in nonhomologous end-joining.
Kaminski et al. (2022)