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Yorodumi- EMDB-17586: E. coli RNA polymerase elongation complex stalled at thymine dime... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17586 | |||||||||
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Title | E. coli RNA polymerase elongation complex stalled at thymine dimer lesion | |||||||||
Map data | Relion4 Postprocessed EM map of E.coli RNAP EC stalled at T=T lesion | |||||||||
Sample |
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Keywords | RNA Polymerase / RNAP / Transcription / Gene Expression / DNA lesion / Stalling | |||||||||
Function / homology | Function and homology information RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / DNA-directed RNA polymerase complex ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Woodgate J / Zenkin N | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nature / Year: 2024 Title: Translation selectively destroys non-functional transcription complexes. Authors: Jason Woodgate / Hamed Mosaei / Pavel Brazda / Flint Stevenson-Jones / Nikolay Zenkin / Abstract: Transcription elongation stalls at lesions in the DNA template. For the DNA lesion to be repaired, the stalled transcription elongation complex (EC) has to be removed from the damaged site. Here we ...Transcription elongation stalls at lesions in the DNA template. For the DNA lesion to be repaired, the stalled transcription elongation complex (EC) has to be removed from the damaged site. Here we show that translation, which is coupled to transcription in bacteria, actively dislodges stalled ECs from the damaged DNA template. By contrast, paused, but otherwise elongation-competent, ECs are not dislodged by the ribosome. Instead, they are helped back into processive elongation. We also show that the ribosome slows down when approaching paused, but not stalled, ECs. Our results indicate that coupled ribosomes functionally and kinetically discriminate between paused ECs and stalled ECs, ensuring the selective destruction of only the latter. This functional discrimination is controlled by the RNA polymerase's catalytic domain, the Trigger Loop. We show that the transcription-coupled DNA repair helicase UvrD, proposed to cause backtracking of stalled ECs, does not interfere with ribosome-mediated dislodging. By contrast, the transcription-coupled DNA repair translocase Mfd acts synergistically with translation, and dislodges stalled ECs that were not destroyed by the ribosome. We also show that a coupled ribosome efficiently destroys misincorporated ECs that can cause conflicts with replication. We propose that coupling to translation is an ancient and one of the main mechanisms of clearing non-functional ECs from the genome. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17586.map.gz | 33.3 MB | EMDB map data format | |
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Header (meta data) | emd-17586-v30.xml emd-17586.xml | 28.3 KB 28.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17586_fsc.xml | 17.8 KB | Display | FSC data file |
Images | emd_17586.png | 198.8 KB | ||
Masks | emd_17586_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-17586.cif.gz | 9 KB | ||
Others | emd_17586_additional_1.map.gz emd_17586_half_map_1.map.gz emd_17586_half_map_2.map.gz | 384.3 MB 385.4 MB 385.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17586 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17586 | HTTPS FTP |
-Related structure data
Related structure data | 8pblMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17586.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Relion4 Postprocessed EM map of E.coli RNAP EC stalled at T=T lesion | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.574 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17586_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Relion4 Refine3D Full EM map of E.coli RNAP EC stalled at T=T lesion
File | emd_17586_additional_1.map | ||||||||||||
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Annotation | Relion4 Refine3D Full EM map of E.coli RNAP EC stalled at T=T lesion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Relion4 Refine3D Half-map 1 of E.coli RNAP EC stalled at T=T lesion
File | emd_17586_half_map_1.map | ||||||||||||
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Annotation | Relion4 Refine3D Half-map 1 of E.coli RNAP EC stalled at T=T lesion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Relion4 Refine3D Half-map 2 of E.coli RNAP EC stalled at T=T lesion
File | emd_17586_half_map_2.map | ||||||||||||
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Annotation | Relion4 Refine3D Half-map 2 of E.coli RNAP EC stalled at T=T lesion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : E. coli RNA Polymerase stalled at T=T lesion.
+Supramolecule #1: E. coli RNA Polymerase stalled at T=T lesion.
+Macromolecule #1: Non-template DNA
+Macromolecule #2: Template DNA
+Macromolecule #3: DNA-directed RNA polymerase subunit alpha
+Macromolecule #4: DNA-directed RNA polymerase subunit beta
+Macromolecule #5: DNA-directed RNA polymerase subunit beta'
+Macromolecule #6: DNA-directed RNA polymerase subunit omega
+Macromolecule #7: mRNA
+Macromolecule #8: ZINC ION
+Macromolecule #9: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 250 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.00026000000000000003 kPa / Details: Positive Charge |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 240000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 16264 / Average exposure time: 3.2 sec. / Average electron dose: 50.0 e/Å2 |