9BH7 | pdb_00009bh7

Human DNA polymerase theta helicase domain dimer in the apo form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Human polymerase theta helicase positions DNA microhomologies for double-strand break repair.

Zerio, C.J.Bai, Y.Sosa-Alvarado, B.A.Guzi, T.Lander, G.C.

(2025) Nat Struct Mol Biol 32: 1061-1068

  • DOI: https://doi.org/10.1038/s41594-025-01514-8
  • Primary Citation of Related Structures:  
    9BH6, 9BH7, 9BH8, 9BH9, 9BHA

  • PubMed Abstract: 

    DNA double-strand breaks occur daily in all human cells and must be repaired with high fidelity to minimize genomic instability. Deficiencies in high-fidelity DNA repair by homologous recombination lead to dependence on DNA polymerase θ, which identifies DNA microhomologies in 3' single-stranded DNA overhangs and anneals them to initiate error-prone double-strand break repair. The resulting genomic instability is associated with numerous cancers, thereby making this polymerase an attractive therapeutic target. However, despite the biomedical importance of polymerase θ, the molecular details of how it initiates DNA break repair remain unclear. Here, we present cryo-electron microscopy structures of the polymerase θ helicase domain bound to microhomology-containing DNA, revealing DNA-induced rearrangements of the helicase that enable DNA repair. Our structures show that DNA-bound helicase dimers facilitate a microhomology search that positions 3' single-stranded DNA ends in proximity to align complementary bases and anneal DNA microhomology. We characterize the molecular determinants that enable the helicase domain of polymerase θ to identify and pair DNA microhomologies to initiate mutagenic DNA repair, thereby providing insight into potentially targetable interactions for therapeutic interventions.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase theta
A, B
893Homo sapiensMutation(s): 0 
Gene Names: POLQPOLH
EC: 3.6.4.12 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 2.7.7.49 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O75417 (Homo sapiens)
Explore O75417 
Go to UniProtKB:  O75417
PHAROS:  O75417
GTEx:  ENSG00000051341 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75417
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC4.3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesF32CA288144
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10OD032467

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-06-25
    Changes: Data collection, Database references