5Y3R

Cryo-EM structure of Human DNA-PK Holoenzyme

Summary for 5Y3R

• Entry DOI: 10.2210/pdb5y3r/pdb
• EMDB information: 6803
• Descriptor: X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, PRKDC-Helix, ... (6 entities in total)
• Functional Keywords: cryo-em structure, dna-pk, dnapkcs, activation, nhej, dna binding protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 6
• Total formula weight: 610106.80

Authors

Yin, X.,Liu, M.,Tian, Y.,Wang, J.,Xu, Y. (deposition date: 2017-07-29, release date: 2017-09-06, Last modification date: 2024-03-27)

Primary citation

Yin, X.,Liu, M.,Tian, Y.,Wang, J.,Xu, Y.
Cryo-EM structure of human DNA-PK holoenzyme
Cell Res., 27:1341-1350, 2017

PubMed Abstract: DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ), the major DNA repair pathway. Here, we determined cryo-electron microscopy structure of human DNA-PK holoenzyme at 6.6 Å resolution. In the complex structure, DNA-PKcs, KU70, KU80 and DNA duplex form a 650-kDa heterotetramer with 1:1:1:1 stoichiometry. The N-terminal α-solenoid (∼2 800 residues) of DNA-PKcs adopts a double-ring fold and connects the catalytic core domain of DNA-PKcs and KU70/80-DNA. DNA-PKcs and KU70/80 together form a DNA-binding tunnel, which cradles ∼30-bp DNA and prevents sliding inward of DNA-PKcs along with DNA duplex, suggesting a mechanism by which the broken DNA end is protected from unnecessary processing. Structural and biochemical analyses indicate that KU70/80 and DNA coordinately induce conformational changes of DNA-PKcs and allosterically stimulate its kinase activity. We propose a model for activation of DNA-PKcs in which allosteric signals are generated upon DNA-PK holoenzyme formation and transmitted to the kinase domain through N-terminal HEAT repeats and FAT domain of DNA-PKcs. Our studies suggest a mechanism for recognition and protection of broken DNA ends and provide a structural basis for understanding the activation of DNA-PKcs and DNA-PK-mediated NHEJ pathway.

PubMed: 28840859
DOI: 10.1038/cr.2017.110

Experimental method

ELECTRON MICROSCOPY (6.6 Å)