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Yorodumi- EMDB-14392: Composite map of two E. coli Mre11-Rad50 (SbcCD) complexes bound ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14392 | |||||||||
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Title | Composite map of two E. coli Mre11-Rad50 (SbcCD) complexes bound to Ku70/80 blocked dsDNA in endonuclease state | |||||||||
Map data | Composite map | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) / Chaetomium thermophilum (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 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_14392.map.gz | 392.9 MB | EMDB map data format | |
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Header (meta data) | emd-14392-v30.xml emd-14392.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_14392.png | 124.4 KB | ||
Masks | emd_14392_msk_1.map | 824 MB | Mask map | |
Others | emd_14392_additional_1.map.gz emd_14392_half_map_1.map.gz emd_14392_half_map_2.map.gz | 404.8 MB 765.6 MB 765.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14392 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14392 | HTTPS FTP |
-Validation report
Summary document | emd_14392_validation.pdf.gz | 944.1 KB | Display | EMDB validaton report |
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Full document | emd_14392_full_validation.pdf.gz | 943.6 KB | Display | |
Data in XML | emd_14392_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | emd_14392_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14392 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14392 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14392.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map | ||||||||||||||||||||||||||||||||||||
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_14392_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_14392_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14392_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14392_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ku-RM-MR-Ku state of two Mre11-Rad50 complexes bound to Ku70/80 b...
Entire | Name: Ku-RM-MR-Ku state of two Mre11-Rad50 complexes bound to Ku70/80 blocked double-stranded DNA |
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Components |
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-Supramolecule #1: Ku-RM-MR-Ku state of two Mre11-Rad50 complexes bound to Ku70/80 b...
Supramolecule | Name: Ku-RM-MR-Ku state of two Mre11-Rad50 complexes bound to Ku70/80 blocked double-stranded DNA type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Supramolecule #2: E. coli Mre11-Rad50 (SbcCD) bound to dsDNA
Supramolecule | Name: E. coli Mre11-Rad50 (SbcCD) bound to dsDNA / type: complex / Chimera: Yes / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: C. thermophilum Ku70/80 bound to dsDNA
Supramolecule | Name: C. thermophilum Ku70/80 bound to dsDNA / type: complex / Chimera: Yes / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
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 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10494 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |