9C5Q

Human DNA polymerase theta helicase domain in microhomology annealed state 2, dimer form

Summary for 9C5Q

• Entry DOI: 10.2210/pdb9c5q/pdb
• EMDB information: 45218
• Descriptor: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*CP*GP*GP*G)-3'), DNA polymerase theta (2 entities in total)
• Functional Keywords: dna repair, helicase, atpase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 192667.09

Authors

Ito, F.,Li, Z.,Chen, X.S. (deposition date: 2024-06-06, release date: 2024-06-26, Last modification date: 2025-04-30)

Primary citation

Ito, F.,Li, Z.,Minakhin, L.,Khant, H.A.,Pomerantz, R.T.,Chen, X.S.
Structural basis for Pol theta-helicase DNA binding and microhomology-mediated end-joining.
Nat Commun, 16:3725-3725, 2025

PubMed Abstract: DNA double-strand breaks (DSBs) present a critical threat to genomic integrity, often precipitating genomic instability and oncogenesis. Repair of DSBs predominantly occurs through homologous recombination (HR) and non-homologous end joining (NHEJ). In HR-deficient cells, DNA polymerase theta (Polθ) becomes critical for DSB repair via microhomology-mediated end joining (MMEJ), also termed theta-mediated end joining (TMEJ). Thus, Polθ is synthetically lethal with BRCA1/2 and other HR factors, underscoring its potential as a therapeutic target in HR-deficient cancers. However, the molecular mechanisms governing Polθ-mediated MMEJ remain poorly understood. Here we present a series of cryo-electron microscopy structures of the Polθ helicase domain (Polθ-hel) in complex with DNA containing different 3'-ssDNA overhangs. The structures reveal the sequential conformations adopted by Polθ-hel during the critical phases of DNA binding, microhomology searching, and microhomology annealing. The stepwise conformational changes within the Polθ-hel subdomains and its functional dimeric state are pivotal for aligning the 3'-ssDNA overhangs, facilitating the microhomology search and subsequent annealing necessary for DSB repair via MMEJ. Our findings illustrate the essential molecular switches within Polθ-hel that orchestrate the MMEJ process in DSB repair, laying the groundwork for the development of targeted therapies against the Polθ-hel.

PubMed: 40253368
DOI: 10.1038/s41467-025-58441-x

Experimental method

ELECTRON MICROSCOPY (3.1 Å)