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Yorodumi- EMDB-40554: Cryo-EM Consensus map of the E. coli transcription-translation co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40554 | |||||||||
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Title | Cryo-EM Consensus map of the E. coli transcription-translation complex (RNAP in an anti-swiveled conformation) | |||||||||
Map data | Cryo-EM Consensus map of the E. coli transcription-translation complex (RNAP in an anti-swiveled conformation) | |||||||||
Sample |
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Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Florez Ariza A / Wee L / Tong A / Canari C / Grob P / Nogales E / Bustamante C | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Cell / Year: 2023 Title: A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Authors: Liang Meng Wee / Alexander B Tong / Alfredo Jose Florez Ariza / Cristhian Cañari-Chumpitaz / Patricia Grob / Eva Nogales / Carlos J Bustamante / Abstract: In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, ...In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40554.map.gz | 260.8 MB | EMDB map data format | |
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Header (meta data) | emd-40554-v30.xml emd-40554.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40554_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_40554.png | 41.2 KB | ||
Masks | emd_40554_msk_1.map | 325 MB | Mask map | |
Others | emd_40554_half_map_1.map.gz emd_40554_half_map_2.map.gz | 261.2 MB 261.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40554 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40554 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40554.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM Consensus map of the E. coli transcription-translation complex (RNAP in an anti-swiveled conformation) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.447 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40554_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half-map 1
File | emd_40554_half_map_1.map | ||||||||||||
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Annotation | half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 2
File | emd_40554_half_map_2.map | ||||||||||||
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Annotation | half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM Consensus map of the E. coli transcription-translation co...
Entire | Name: Cryo-EM Consensus map of the E. coli transcription-translation complex (RNAP in an anti-swiveled conformation) |
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Components |
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-Supramolecule #1: Cryo-EM Consensus map of the E. coli transcription-translation co...
Supramolecule | Name: Cryo-EM Consensus map of the E. coli transcription-translation complex (RNAP in an anti-swiveled conformation) type: complex / ID: 1 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 2 MDa |
-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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Grid | Model: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |