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Yorodumi- EMDB-14159: Cryo-EM reconstruction of the Bacillus subtilis MutS2-collided di... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14159 | |||||||||
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Title | Cryo-EM reconstruction of the Bacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information mismatch repair complex / mismatched DNA binding / negative regulation of DNA recombination / positive regulation of rRNA processing / nucleoid / mismatch repair / ATP-dependent activity, acting on DNA / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly ...mismatch repair complex / mismatched DNA binding / negative regulation of DNA recombination / positive regulation of rRNA processing / nucleoid / mismatch repair / ATP-dependent activity, acting on DNA / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / endonuclease activity / tRNA binding / negative regulation of translation / Hydrolases; Acting on ester bonds / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.14 Å | |||||||||
Authors | Filbeck S / Pfeffer S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nature / Year: 2022 Title: Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue. Authors: Federico Cerullo / Sebastian Filbeck / Pratik Rajendra Patil / Hao-Chih Hung / Haifei Xu / Julia Vornberger / Florian W Hofer / Jaro Schmitt / Guenter Kramer / Bernd Bukau / Kay Hofmann / ...Authors: Federico Cerullo / Sebastian Filbeck / Pratik Rajendra Patil / Hao-Chih Hung / Haifei Xu / Julia Vornberger / Florian W Hofer / Jaro Schmitt / Guenter Kramer / Bernd Bukau / Kay Hofmann / Stefan Pfeffer / Claudio A P Joazeiro / Abstract: Ribosome stalling during translation is detrimental to cellular fitness, but how this is sensed and elicits recycling of ribosomal subunits and quality control of associated mRNA and incomplete ...Ribosome stalling during translation is detrimental to cellular fitness, but how this is sensed and elicits recycling of ribosomal subunits and quality control of associated mRNA and incomplete nascent chains is poorly understood. Here we uncover Bacillus subtilis MutS2, a member of the conserved MutS family of ATPases that function in DNA mismatch repair, as an unexpected ribosome-binding protein with an essential function in translational quality control. Cryo-electron microscopy analysis of affinity-purified native complexes shows that MutS2 functions in sensing collisions between stalled and translating ribosomes and suggests how ribosome collisions can serve as platforms to deploy downstream processes: MutS2 has an RNA endonuclease small MutS-related (SMR) domain, as well as an ATPase/clamp domain that is properly positioned to promote ribosomal subunit dissociation, which is a requirement both for ribosome recycling and for initiation of ribosome-associated protein quality control (RQC). Accordingly, MutS2 promotes nascent chain modification with alanine-tail degrons-an early step in RQC-in an ATPase domain-dependent manner. The relevance of these observations is underscored by evidence of strong co-occurrence of MutS2 and RQC genes across bacterial phyla. Overall, the findings demonstrate a deeply conserved role for ribosome collisions in mounting a complex response to the interruption of translation within open reading frames. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_14159.map.gz | 104.3 MB | EMDB map data format | |
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Header (meta data) | emd-14159-v30.xml emd-14159.xml | 66.9 KB 66.9 KB | Display Display | EMDB header |
Images | emd_14159.png | 148 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14159 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14159 | HTTPS FTP |
-Related structure data
Related structure data | 7qv3MC 7qv1C 7qv2C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14159.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.605 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Collided disome from Bacillus subtilis
+Supramolecule #1: Collided disome from Bacillus subtilis
+Macromolecule #1: 50S ribosomal protein L32
+Macromolecule #2: 50S ribosomal protein L33 1
+Macromolecule #3: 50S ribosomal protein L34
+Macromolecule #4: 50S ribosomal protein L35
+Macromolecule #5: 50S ribosomal protein L36
+Macromolecule #6: 50S ribosomal protein L31
+Macromolecule #9: 50S ribosomal protein L2
+Macromolecule #10: 50S ribosomal protein L3
+Macromolecule #11: 50S ribosomal protein L4
+Macromolecule #12: 50S ribosomal protein L5
+Macromolecule #13: 50S ribosomal protein L6
+Macromolecule #15: Nascent chain
+Macromolecule #16: 50S ribosomal protein L13
+Macromolecule #17: 50S ribosomal protein L14
+Macromolecule #18: 50S ribosomal protein L15
+Macromolecule #19: 50S ribosomal protein L16
+Macromolecule #20: 50S ribosomal protein L17
+Macromolecule #21: 50S ribosomal protein L18
+Macromolecule #22: 50S ribosomal protein L19
+Macromolecule #23: 50S ribosomal protein L20
+Macromolecule #24: 50S ribosomal protein L21
+Macromolecule #25: 50S ribosomal protein L22
+Macromolecule #26: 50S ribosomal protein L23
+Macromolecule #27: 50S ribosomal protein L24
+Macromolecule #29: 50S ribosomal protein L27
+Macromolecule #30: 50S ribosomal protein L9
+Macromolecule #31: 50S ribosomal protein L29
+Macromolecule #32: 50S ribosomal protein L30
+Macromolecule #34: 30S ribosomal protein S21
+Macromolecule #35: 30S ribosomal protein S3
+Macromolecule #36: 30S ribosomal protein S4
+Macromolecule #37: 30S ribosomal protein S5
+Macromolecule #38: 30S ribosomal protein S6
+Macromolecule #39: 30S ribosomal protein S7
+Macromolecule #40: 30S ribosomal protein S8
+Macromolecule #41: 30S ribosomal protein S9
+Macromolecule #42: 30S ribosomal protein S10
+Macromolecule #43: 30S ribosomal protein S11
+Macromolecule #44: 30S ribosomal protein S12
+Macromolecule #45: 30S ribosomal protein S13
+Macromolecule #46: 30S ribosomal protein S14
+Macromolecule #47: 30S ribosomal protein S15
+Macromolecule #48: 30S ribosomal protein S16
+Macromolecule #49: 30S ribosomal protein S17
+Macromolecule #50: 30S ribosomal protein S18
+Macromolecule #51: 30S ribosomal protein S19
+Macromolecule #52: 30S ribosomal protein S20
+Macromolecule #53: 50S ribosomal protein L28
+Macromolecule #54: Endonuclease MutS2
+Macromolecule #7: mRNA
+Macromolecule #8: 5S ribosomal RNA
+Macromolecule #14: P-site tRNA
+Macromolecule #28: 23S ribosomal RNA
+Macromolecule #33: 16S ribosomal RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 8297591 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: OTHER Details: Internal Cryo-EM reconstruction of the 70S ribosome |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 5078 |