1Z56

Co-Crystal Structure of Lif1p-Lig4p

• PDB DOI: https://doi.org/10.2210/pdb1Z56/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): No 


• Deposited: 2005-03-17 Released: 2006-01-31 
• Deposition Author(s): Dore, A.S., Furnham, N., Davies, O.R., Sibanda, B.L., Chirgadze, D.Y., Jackson, S.P., Pellegrini, L., Blundell, T.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.92 Å
• R-Value Free: 0.467 
• R-Value Work: 0.400 
• R-Value Observed: 0.403 

Literature

Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode.

Dore, A.S., Furnham, N., Davies, O.R., Sibanda, B.L., Chirgadze, D.Y., Jackson, S.P., Pellegrini, L., Blundell, T.L.

(2006) DNA Repair (Amst) 5: 362-368

• PubMed: 16388993 
• DOI: https://doi.org/10.1016/j.dnarep.2005.11.004
• Primary Citation of Related Structures:  
  1Z56


• PubMed Abstract: 
  

  DNA ligase IV catalyses the final ligation step in the non-homologous end-joining (NHEJ) DNA repair pathway and requires interaction of the ligase with the Xrcc4 'genome-guardian', an essential NHEJ factor. Here we report the 3.9 A crystal structure of the Saccharomyces cerevisiae Xrcc4 ortholog ligase interacting factor 1 (Lif1p) complexed with the C-terminal BRCT domains of DNA ligase IV (Lig4p). The structure reveals a novel mode of protein recognition by a tandem BRCT repeat, and in addition provides a molecular basis for a human LIG4 syndrome clinical condition.

---

Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 11-mer - A3B2C2D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 11-mer - A2B1C1D1E1F1G1H1I1J1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 102.07 kDa 
• Atom Count: 4,164 
• Modelled Residue Count: 557 
• Deposited Residue Count: 923 
• Unique protein chains: 9

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase interacting factor 1	A, B	246	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIF1
UniProt
Find proteins for P53150 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53150  Go to UniProtKB:  P53150

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase IV	C	264	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: DNL4, LIG4 EC: 6.5.1.1
UniProt
Find proteins for Q08387 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08387  Go to UniProtKB:  Q08387

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase interacting factor 1	D	8	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIF1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase interacting factor 1	E, H	7	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIF1

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase interacting factor 1	F	45	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIF1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase interacting factor 1	G	37	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIF1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase interacting factor 1	I	30	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIF1

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase interacting factor 1	J	20	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIF1

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase interacting factor 1	K	13	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIF1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.92 Å
• R-Value Free: 0.467 
• R-Value Work: 0.400 
• R-Value Observed: 0.403 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 247.617	α = 90
b = 247.617	β = 90
c = 98.416	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-31 
Deposition Author(s): Dore, A.S., Furnham, N., Davies, O.R., Sibanda, B.L., Chirgadze, D.Y., Jackson, S.P., Pellegrini, L., Blundell, T.L.

Revision History  

• Version 1.0: 2006-01-31
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations