› 6q1v

X-ray diffraction
1.85Å resolution

Human DNA Ligase 1 (E592R) Bound to an Adenylated, hydroxyl terminated DNA nick

Released:
DOI: 10.2210/pdb6q1v/pdb
PDB entry 6q1v coloured by chain, front view.
PDB entry 6q1v coloured by chain, side view.
PDB entry 6q1v coloured by chain, top view.
Source organisms:
Primary publication:
Two-tiered enforcement of high-fidelity DNA ligation.
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS
Nat Commun 10 5431 (2019)
PMID: 31780661

Function and Biology Details

Reaction catalysed: 
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
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-120479 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA ligase 1 Chain: A
Molecule details ›
Chain: A
Length: 645 amino acids
Theoretical weight: 71.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P18858 (Residues: 262-904; Coverage: 70%)
Gene name: LIG1
Sequence domains:
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2.14 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.49 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand PEG 1 x PEG
Ligand ACT 1 x ACT
Ligand AMP 1 x AMP
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 71.486Å b: 101.171Å c: 115.291Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.162 0.194
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

XRCC1 - Strategies for coordinating and assembling a versatile DNA damage response.
London RE. (2020)
1 more

1 mention without citation

Two-tiered enforcement of high-fidelity DNA ligation.
Tumbale et al. (2019)