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TitleCryo-EM structures of NHEJ assemblies with nucleosomes.
Journal, issue, pagesNat Commun, Year 2025
Publish dateDec 24, 2025
AuthorsChloe Hall / Philippe Frit / Antonia Kefala-Stavridi / Amandine Pelletier / Steven W Hardwick / Himani Amin / Matthew K Bilyard / Taiana Maia De Oliviera / Ammarah Tariq / Sayma Zahid / Dimitri Y Chirgadze / Shankar Balasubramanian / Katheryn Meek / Virginie Ropars / Jean-Baptiste Charbonnier / Mauro Modesti / Patrick Calsou / Sébastien Britton / Tom L Blundell / Thomas Schalch / Amanda K Chaplin /
PubMed AbstractDNA double-strand breaks (DSBs) are highly deleterious lesions that can trigger cell death or carcinogenesis if unrepaired or misrepaired. In mammals, most DSBs are repaired by non-homologous end ...DNA double-strand breaks (DSBs) are highly deleterious lesions that can trigger cell death or carcinogenesis if unrepaired or misrepaired. In mammals, most DSBs are repaired by non-homologous end joining (NHEJ), which begins when Ku70/80 binds DNA ends and recruits DNA-PKcs to form the DNA-PK holoenzyme. Although recent cryo-EM studies have resolved several NHEJ assemblies, how these factors access DSBs within nucleosomes remains unclear. Here, we present cryo-EM structures of human Ku70/80 and DNA-PK bound to nucleosomes. Ku70/80 binds the DNA end and bends it away from the nucleosome core, while the Ku70 C-terminal SAP domain makes an additional, specific DNA contact. Our DNA-PK-nucleosome structure further reveals the opening of the Ku80 vWA domain, and we show that non-hydrolysable ATP promotes synapsis by stabilising the Ku80-mediated DNA-PK dimer. These structures reveal a model for DSB recognition on nucleosomal DNA and provide insights relevant to targeting NHEJ in cancer therapy.
External linksNat Commun / PubMed:41444611
MethodsEM (single particle)
Resolution2.94 - 5.0 Å
Structure data

52860

9igw

EMDB-52860, PDB-9igw:
Ku70/80 bound to 147 bp nucleosome
Method: EM (single particle) / Resolution: 3.32 Å

52861

9igx

EMDB-52861, PDB-9igx:
Ku70/80 bound to 153 bp nucleosome
Method: EM (single particle) / Resolution: 3.56 Å

52879

9q80

EMDB-52879, PDB-9q80:
Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome
Method: EM (single particle) / Resolution: 3.39 Å

52912

9q8x

EMDB-52912, PDB-9q8x:
Ku70/80 bound to a 153 bp H2AX nucleosome
Method: EM (single particle) / Resolution: 2.94 Å

52958

9q9f

EMDB-52958, PDB-9q9f:
DNA-PK bound to a 153 bp H2AX nucleosome model 1
Method: EM (single particle) / Resolution: 4.54 Å

53025

9qcr

EMDB-53025, PDB-9qcr:
DNA-PK bound to 153 bp H2AX nucleosome model 2
Method: EM (single particle) / Resolution: 4.37 Å

53026

9qcs

EMDB-53026, PDB-9qcs:
Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome
Method: EM (single particle) / Resolution: 4.38 Å

53237

9qms

EMDB-53237, PDB-9qms:
DNA-PK bound to 153 bp H2AX nucleosome with ATPyS
Method: EM (single particle) / Resolution: 5.0 Å

Source
  • homo sapiens (human)
KeywordsDNA BINDING PROTEIN / DNA-binding protein / NHEJ / Ku70/80 / nucleosome

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