3RWR | pdb_00003rwr

Crystal structure of the human XRCC4-XLF complex

• PDB DOI: https://doi.org/10.2210/pdb3RWR/pdb

• Classification: DNA binding protein/protein binding
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-09 Released: 2011-12-07 
• Deposition Author(s): Andres, S.N., Junop, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.94 Å
• R-Value Free: 
  0.326 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.271 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Literature

Structure of human XLF-XRCC4: assembly of a functional DNA repair complex

Andres, N.S., Wyman, C., Modesti, M., Junop, M.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A4B4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 558.22 kDa 
• Atom Count: 36,833 
• Modeled Residue Count: 4,581 
• Deposited Residue Count: 4,716 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC4	A, B, E [auth F], F [auth G], I [auth J], J [auth K], M [auth N], N [auth P], Q [auth R], R [auth V], W [auth U], X [auth Y]	163	Homo sapiens	Mutation(s): 0  Gene Names: XRCC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13426 (Homo sapiens) Explore Q13426  Go to UniProtKB:  Q13426
PHAROS:  Q13426 GTEx:  ENSG00000152422

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-homologous end-joining factor 1	C [auth D], D [auth E], G [auth H], H [auth I], K [auth L], L [auth M], O, P [auth Q], S, T [auth W], U [auth T], V [auth X]	230	Homo sapiens	Mutation(s): 0  Gene Names: NHEJ1, XLF
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Q4 (Homo sapiens) Explore Q9H9Q4  Go to UniProtKB:  Q9H9Q4
PHAROS:  Q9H9Q4 GTEx:  ENSG00000187736

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBR	AA [auth J], BA [auth M], CA [auth P], DA [auth V], EA [auth X], FA [auth Y], Y [auth D], Z [auth H]	HEXATANTALUM DODECABROMIDE Br12 Ta6 YWYIQTPPCOBSGN-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.94 Å
• R-Value Free:  0.326 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.271 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 745.379	α = 90
b = 149.585	β = 94.72
c = 80.475	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
CBASS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Andres, S.N., Junop, M.S.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2014-10-29
  Changes: Structure summary
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations