[English] 日本語
Yorodumi- EMDB-45217: Human DNA polymerase theta helicase domain in microhomology annea... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45217 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human DNA polymerase theta helicase domain in microhomology annealed state 1, dimer form | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | DNA repair / helicase / ATPase / TRANSFERASE-DNA complex / DNA BINDING PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Ito F / Li Z / Chen XS | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: bioRxiv / Year: 2024 Title: Structural Basis for Polθ-Helicase DNA Binding and Microhomology-Mediated End-Joining. Authors: Fumiaki Ito / Ziyuan Li / Leonid Minakhin / Htet A Khant / Richard T Pomerantz / Xiaojiang S Chen / 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 ...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 3'-overhang. 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'-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. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_45217.map.gz | 63.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-45217-v30.xml emd-45217.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45217_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_45217.png | 122.8 KB | ||
Filedesc metadata | emd-45217.cif.gz | 4 KB | ||
Others | emd_45217_half_map_1.map.gz emd_45217_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45217 | HTTPS FTP |
-Validation report
Summary document | emd_45217_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_45217_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_45217_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_45217_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45217 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_45217.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_45217_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_45217_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human DNA polymerase theta helicase domain in microhomology annea...
Entire | Name: Human DNA polymerase theta helicase domain in microhomology annealed state 1, dimer form |
---|---|
Components |
|
-Supramolecule #1: Human DNA polymerase theta helicase domain in microhomology annea...
Supramolecule | Name: Human DNA polymerase theta helicase domain in microhomology annealed state 1, dimer form type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 253 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
---|---|
Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10331 / Average exposure time: 3.5 sec. / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |