+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14394 | |||||||||
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Title | C. thermophilum Ku70/80 heterodimer bound to DNA | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Chaetomium ther (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Gut F / Kaeshammer L / Lammens K / Bartho J / van de Logt E / Kessler B / Hopfner KP | |||||||||
Funding support | European Union, Germany, 2 items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Authors: Fabian Gut / Lisa Käshammer / Katja Lammens / Joseph D Bartho / Anna-Maria Boggusch / Erik van de Logt / Brigitte Kessler / Karl-Peter Hopfner / Abstract: DNA double-strand breaks (DSBs) threaten genome stability and are linked to tumorigenesis in humans. Repair of DSBs requires the removal of attached proteins and hairpins through a poorly understood ...DNA double-strand breaks (DSBs) threaten genome stability and are linked to tumorigenesis in humans. Repair of DSBs requires the removal of attached proteins and hairpins through a poorly understood but physiologically critical endonuclease activity by the Mre11-Rad50 complex. Here, we report cryoelectron microscopy (cryo-EM) structures of the bacterial Mre11-Rad50 homolog SbcCD bound to a protein-blocked DNA end and a DNA hairpin. The structures reveal that Mre11-Rad50 bends internal DNA for endonucleolytic cleavage and show how internal DNA, DNA ends, and hairpins are processed through a similar ATP-regulated conformational state. Furthermore, Mre11-Rad50 is loaded onto blocked DNA ends with Mre11 pointing away from the block, explaining the distinct biochemistries of 3' → 5' exonucleolytic and endonucleolytic incision through the way Mre11-Rad50 interacts with diverse DNA ends. In summary, our results unify Mre11-Rad50's enigmatic nuclease diversity within a single structural framework and reveal how blocked DNA ends and hairpins are processed. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14394.map.gz | 6.4 MB | EMDB map data format | |
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Header (meta data) | emd-14394-v30.xml emd-14394.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14394_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_14394.png | 58.4 KB | ||
Masks | emd_14394_msk_1.map | 125 MB | Mask map | |
Others | emd_14394_half_map_1.map.gz emd_14394_half_map_2.map.gz | 24.8 MB 24.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14394 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14394 | HTTPS FTP |
-Validation report
Summary document | emd_14394_validation.pdf.gz | 535 KB | Display | EMDB validaton report |
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Full document | emd_14394_full_validation.pdf.gz | 534.6 KB | Display | |
Data in XML | emd_14394_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_14394_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14394 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14394 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14394.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14394_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14394_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14394_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Heterodimer of C. thermophilum Ku70/80 bound to double-stranded DNA
Entire | Name: Heterodimer of C. thermophilum Ku70/80 bound to double-stranded DNA |
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Components |
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-Supramolecule #1: Heterodimer of C. thermophilum Ku70/80 bound to double-stranded DNA
Supramolecule | Name: Heterodimer of C. thermophilum Ku70/80 bound to double-stranded DNA type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Chaetomium ther (E. coli) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.19 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |