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- EMDB-14392: Composite map of two E. coli Mre11-Rad50 (SbcCD) complexes bound ... -
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Open data
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Basic information
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Title | Composite map of two E. coli Mre11-Rad50 (SbcCD) complexes bound to Ku70/80 blocked dsDNA in endonuclease state | |||||||||
![]() | Composite map | |||||||||
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Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
![]() | Gut F / Kaeshammer L / Lammens K / Bartho J / van de Logt E / Kessler B / Hopfner KP | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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 | ![]() | 392.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
Images | ![]() | 124.4 KB | ||
Masks | ![]() | 824 MB | ![]() | |
Others | ![]() ![]() ![]() | 404.8 MB 765.6 MB 765.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 944.1 KB | Display | ![]() |
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Full document | ![]() | 943.6 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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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
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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 |
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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: ![]() ![]() |
-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: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-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: ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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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 |