6ERF

Complex of APLF factor and Ku heterodimer bound to DNA

• PDB DOI:  https://doi.org/10.2210/pdb6ERF/pdb
• NAKB: 6ERF

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-10-18 Released: 2018-10-17 
• Deposition Author(s): Nemoz, C., Legrand, P., Ropars, V., Charbonnier, J.B.
• Funding Organization(s): INCA, French National Research Agency, ARC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.227 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Literature

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining.

Nemoz, C., Ropars, V., Frit, P., Gontier, A., Drevet, P., Yu, J., Guerois, R., Pitois, A., Comte, A., Delteil, C., Barboule, N., Legrand, P., Baconnais, S., Yin, Y., Tadi, S., Barbet-Massin, E., Berger, I., Le Cam, E., Modesti, M., Rothenberg, E., Calsou, P., Charbonnier, J.B.

(2018) Nat Struct Mol Biol 25: 971-980

• PubMed: 30291363 
• DOI: https://doi.org/10.1038/s41594-018-0133-6
• Primary Citation of Related Structures:  
  6ERF, 6ERG, 6ERH


• PubMed Abstract: 
  

The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that remain unclear. We have determined crystal structures of the Ku-binding motifs (KBM) of the NHEJ proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex. The two KBM motifs bind remote sites of the Ku80 α/β domain. The X-KBM occupies an internal pocket formed by an unprecedented large outward rotation of the Ku80 α/β domain. We observe independent recruitment of the APLF-interacting protein XRCC4 and of XLF to laser-irradiated sites via binding of A- and X-KBMs, respectively, to Ku80. Finally, we show that mutation of the X-KBM and A-KBM binding sites in Ku80 compromises both the efficiency and accuracy of end joining and cellular radiosensitivity. A- and X-KBMs may represent two initial anchor points to build the intricate interaction network required for NHEJ.

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Organizational Affiliation: 

Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 588.18 kDa 
• Atom Count: 35,411 
• Modelled Residue Count: 4,233 
• Deposited Residue Count: 4,756 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
X-ray repair cross-complementing protein 6	A, C, E, G	544	Homo sapiens	Mutation(s): 0  Gene Names: XRCC6, G22P1 EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12956 (Homo sapiens) Explore P12956  Go to UniProtKB:  P12956
PHAROS:  P12956

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
X-ray repair cross-complementing protein 5	B, D, F, H	572	Homo sapiens	Mutation(s): 0  Gene Names: XRCC5, G22P2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P13010 (Homo sapiens) Explore P13010  Go to UniProtKB:  P13010
PHAROS:  P13010

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Aprataxin and PNK-like factor	Q, R, S, T	18	Homo sapiens	Mutation(s): 0  Gene Names: APLF, C2orf13, PALF, XIP1 EC: 4.2.99.18 (PDB Primary Data), 3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IW19 (Homo sapiens) Explore Q8IW19  Go to UniProtKB:  Q8IW19
PHAROS:  Q8IW19

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')	I, K, M, O	21	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (34-MER)	J, L, N, P	34	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.227 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.92	α = 68.64
b = 140.86	β = 80.85
c = 150.31	γ = 81.23

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction
STARANISO	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Nemoz, C., Legrand, P., Ropars, V., Charbonnier, J.B.

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Funding Organization	Location	Grant Number
INCA	France	PLBIO 2012-280
French National Research Agency	France	ANR-12-SVSE8-012
ARC	France	SLS220120605310

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2021-06-23
  Changes: Database references, Refinement description