› 1z56

X-ray diffraction
3.92Å resolution

Co-Crystal Structure of Lif1p-Lig4p

Released:
DOI: 10.2210/pdb1z56/pdb
PDB entry 1z56 coloured by chain, front view.
PDB entry 1z56 coloured by chain, side view.
PDB entry 1z56 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode.
Doré AS, Furnham N, Davies OR, Sibanda BL, Chirgadze DY, Jackson SP, Pellegrini L, Blundell TL
DNA Repair (Amst) 5 362-8 (2006)
PMID: 16388993

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 undecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156730 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
Ligase-interacting factor 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 246 amino acids
Theoretical weight: 28.67 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P53150 (Residues: 1-246; Coverage: 58%)
Gene names: LIF1, YGL090W
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
DNA ligase 4 Chain: C
Molecule details ›
Chain: C
Length: 264 amino acids
Theoretical weight: 30.37 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q08387 (Residues: 681-944; Coverage: 28%)
Gene names: DNL4, LIG4, UND407, UNE452, YOR005C
Sequence domains: BRCA1 C Terminus (BRCT) domain
Structure domains: BRCT domain
Ligase interacting factor 1 Chain: D
Molecule details ›
Chain: D
Length: 8 amino acids
Theoretical weight: 699 Da
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
Ligase interacting factor 1 Chains: E, H
Molecule details ›
Chains: E, H
Length: 7 amino acids
Theoretical weight: 614 Da
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
Ligase interacting factor 1 Chain: F
Molecule details ›
Chain: F
Length: 45 amino acids
Theoretical weight: 3.85 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
Ligase interacting factor 1 Chain: G
Molecule details ›
Chain: G
Length: 37 amino acids
Theoretical weight: 3.17 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
Ligase interacting factor 1 Chain: I
Molecule details ›
Chain: I
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
Ligase interacting factor 1 Chain: J
Molecule details ›
Chain: J
Length: 20 amino acids
Theoretical weight: 1.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
Ligase interacting factor 1 Chain: K
Molecule details ›
Chain: K
Length: 13 amino acids
Theoretical weight: 1.12 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID13
Spacegroup: P6422
Unit cell:
a: 247.617Å b: 247.617Å c: 98.416Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.403 0.4 0.467
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli

Quick links

Citations

7 review citations

Repair of double-strand breaks by end joining.
Chiruvella et al. (2013)
6 more

5 mentions without citation

De Novo modeling in cryo-EM density maps with Pathwalking.
Chen et al. (2016)
4 more