6ERG image
Entry Detail
PDB ID:
6ERG
Title:
Complex of XLF and heterodimer Ku bound to DNA
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2017-10-18
Release Date:
2018-10-17
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:X-ray repair cross-complementing protein 6
Chain IDs:A, D
Chain Length:544
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:X-ray repair cross-complementing protein 5
Chain IDs:B, E
Chain Length:572
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Non-homologous end-joining factor 1
Chain IDs:C, F
Chain Length:13
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Description:DNA (21-MER)
Chain IDs:G (auth: H), H (auth: K)
Chain Length:21
Number of Molecules:2
Biological Source:Synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (34-MER)
Chain IDs:I (auth: M), J (auth: R)
Chain Length:34
Number of Molecules:2
Biological Source:Synthetic construct
Ligand Molecules
Primary Citation
XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining.
Nat. Struct. Mol. Biol. 25 971 980 (2018)
PMID: 30291363 DOI: 10.1038/s41594-018-0133-6

Abstact

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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Primary Citation of related structures