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Yorodumi- EMDB-29214: Cryo-EM structure of E. coli 70S Ribosome containing mRNA and tRN... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29214 | |||||||||
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Title | Cryo-EM structure of E. coli 70S Ribosome containing mRNA and tRNA (in the transcription-translation complex) | |||||||||
Map data | Cryo-EM structure of translational competent E. coli 70S Ribosome containing mRNA and tRNA (in the transcription-translation complex) | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / stringent response / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of ribosome biogenesis / translational termination / DnaA-L2 complex / negative regulation of translational initiation / translational initiation ...negative regulation of cytoplasmic translational initiation / stringent response / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of ribosome biogenesis / translational termination / DnaA-L2 complex / negative regulation of translational initiation / translational initiation / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / cytosolic ribosome assembly / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia phage Lambda (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 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_29214.map.gz | 7.2 MB | EMDB map data format | |
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Header (meta data) | emd-29214-v30.xml emd-29214.xml | 66 KB 66 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29214_fsc.xml | 14.7 KB | Display | FSC data file |
Images | emd_29214.png | 66.5 KB | ||
Masks | emd_29214_msk_1.map | 274.6 MB | Mask map | |
Others | emd_29214_half_map_1.map.gz emd_29214_half_map_2.map.gz | 220.7 MB 220.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29214 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29214 | HTTPS FTP |
-Related structure data
Related structure data | 8fizMC 8fixC 8fiyC 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_29214.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of translational competent E. coli 70S Ribosome containing mRNA and tRNA (in the transcription-translation complex) | ||||||||||||||||||||
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_29214_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half-map 1
File | emd_29214_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_29214_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 structure of E. coli 70S Ribosome containing mRNA and tRN...
+Supramolecule #1: Cryo-EM structure of E. coli 70S Ribosome containing mRNA and tRN...
+Macromolecule #1: 16S rRNA
+Macromolecule #23: mRNA
+Macromolecule #24: 23S rRNA
+Macromolecule #25: P-site tRNA
+Macromolecule #26: 5s rRNA
+Macromolecule #2: 30S ribosomal protein S20
+Macromolecule #3: 30S ribosomal protein S12
+Macromolecule #4: 30S ribosomal protein S19
+Macromolecule #5: 30S ribosomal protein S13
+Macromolecule #6: 30S ribosomal protein S14
+Macromolecule #7: 30S ribosomal protein S3
+Macromolecule #8: 30S ribosomal protein S10
+Macromolecule #9: 30S ribosomal protein S4
+Macromolecule #10: 30S ribosomal protein S2
+Macromolecule #11: 30S ribosomal protein S9
+Macromolecule #12: 30S ribosomal protein S7
+Macromolecule #13: 30S ribosomal protein S11
+Macromolecule #14: 30S ribosomal protein S6
+Macromolecule #15: 30S ribosomal protein S16
+Macromolecule #16: 30S ribosomal protein S5
+Macromolecule #17: 30S ribosomal protein S8
+Macromolecule #18: 30S ribosomal protein S15
+Macromolecule #19: 30S ribosomal protein S17
+Macromolecule #20: 30S ribosomal protein S18
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #22: 50S ribosomal protein L31
+Macromolecule #27: 50S ribosomal protein L2
+Macromolecule #28: 50S ribosomal protein L3
+Macromolecule #29: 50S ribosomal protein L4
+Macromolecule #30: 50S ribosomal protein L5
+Macromolecule #31: 50S ribosomal protein L18
+Macromolecule #32: 50S ribosomal protein L33
+Macromolecule #33: 50S ribosomal protein L6
+Macromolecule #34: 50S ribosomal protein L9
+Macromolecule #35: 50S ribosomal protein L11
+Macromolecule #36: 50S ribosomal protein L32
+Macromolecule #37: 50S ribosomal protein L34
+Macromolecule #38: 50S ribosomal protein L35
+Macromolecule #39: 50S ribosomal protein L36
+Macromolecule #40: 50S ribosomal protein L30
+Macromolecule #41: 50S ribosomal protein L13
+Macromolecule #42: 50S ribosomal protein L14
+Macromolecule #43: 50S ribosomal protein L15
+Macromolecule #44: 50S ribosomal protein L16
+Macromolecule #45: 50S ribosomal protein L17
+Macromolecule #46: 50S ribosomal protein L19
+Macromolecule #47: 50S ribosomal protein L20
+Macromolecule #48: Ribosomal protein L21
+Macromolecule #49: 50S ribosomal protein L22
+Macromolecule #50: 50S ribosomal protein L23
+Macromolecule #51: 50S ribosomal protein L24
+Macromolecule #52: 50S ribosomal protein L25
+Macromolecule #53: 50S ribosomal protein L27
+Macromolecule #54: 50S ribosomal protein L28
+Macromolecule #55: 50S ribosomal protein L29
+Macromolecule #56: 50S ribosomal protein L10
-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 |