+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3580 | |||||||||
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Title | E. coli expressome | |||||||||
Map data | E. coli expressome | |||||||||
Sample |
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Keywords | expressome ribosome RNA polymerase / ribosome | |||||||||
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 / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing ...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 / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription initiation / cell motility / DNA-templated transcription termination / maintenance of translational fidelity / ribonucleoside binding / mRNA 5'-UTR binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome biogenesis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / response to heat / cytosolic small ribosomal subunit / protein-containing complex assembly / intracellular iron ion homeostasis / cytoplasmic translation / tRNA binding / molecular adaptor activity / protein dimerization activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / DNA-templated transcription / mRNA binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
Authors | Kohler R / Mooney RA | |||||||||
Citation | Journal: Science / Year: 2017 Title: Architecture of a transcribing-translating expressome. Authors: R Kohler / R A Mooney / D J Mills / R Landick / P Cramer / Abstract: DNA transcription is functionally coupled to messenger RNA (mRNA) translation in bacteria, but how this is achieved remains unclear. Here we show that RNA polymerase (RNAP) and the ribosome of can ...DNA transcription is functionally coupled to messenger RNA (mRNA) translation in bacteria, but how this is achieved remains unclear. Here we show that RNA polymerase (RNAP) and the ribosome of can form a defined transcribing and translating "expressome" complex. The cryo-electron microscopic structure of the expressome reveals continuous protection of ~30 nucleotides of mRNA extending from the RNAP active center to the ribosome decoding center. The RNAP-ribosome interface includes the RNAP subunit α carboxyl-terminal domain, which is required for RNAP-ribosome interaction in vitro and for pronounced cell growth defects upon translation inhibition in vivo, consistent with its function in transcription-translation coupling. The expressome structure can only form during transcription elongation and explains how translation can prevent transcriptional pausing, backtracking, and termination. | |||||||||
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_3580.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-3580-v30.xml emd-3580.xml | 42.3 KB 42.3 KB | Display Display | EMDB header |
Images | emd_3580.png | 58 KB | ||
Filedesc metadata | emd-3580.cif.gz | 10.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3580 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3580 | HTTPS FTP |
-Validation report
Summary document | emd_3580_validation.pdf.gz | 227 KB | Display | EMDB validaton report |
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Full document | emd_3580_full_validation.pdf.gz | 226.1 KB | Display | |
Data in XML | emd_3580_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3580 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3580 | HTTPS FTP |
-Related structure data
Related structure data | 5my1MC 3579C M: atomic model generated by this map C: citing same article (ref.) |
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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_3580.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E. coli expressome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.84 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 : in vitro reconstituted E. coli expressome consisting of transcrib...
+Supramolecule #1: in vitro reconstituted E. coli expressome consisting of transcrib...
+Supramolecule #2: Translating Ribosome
+Supramolecule #3: Transcribing RNA Polymerase
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S3
+Macromolecule #3: 30S ribosomal protein S4
+Macromolecule #4: 30S ribosomal protein S5
+Macromolecule #5: 30S ribosomal protein S6
+Macromolecule #6: 30S ribosomal protein S7
+Macromolecule #7: 30S ribosomal protein S8
+Macromolecule #8: 30S ribosomal protein S9
+Macromolecule #9: 30S ribosomal protein S10
+Macromolecule #10: 30S ribosomal protein S11
+Macromolecule #11: 30S ribosomal protein S12
+Macromolecule #12: 30S ribosomal protein S13
+Macromolecule #13: 30S ribosomal protein S14
+Macromolecule #14: 30S ribosomal protein S15
+Macromolecule #15: 30S ribosomal protein S16
+Macromolecule #16: 30S ribosomal protein S17
+Macromolecule #17: 30S ribosomal protein S18
+Macromolecule #18: 30S ribosomal protein S19
+Macromolecule #19: 30S ribosomal protein S20
+Macromolecule #20: 30S ribosomal protein S2
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #22: DNA-directed RNA polymerase subunit alpha
+Macromolecule #23: DNA-directed RNA polymerase subunit beta
+Macromolecule #24: DNA-directed RNA polymerase subunit beta'
+Macromolecule #25: DNA-directed RNA polymerase subunit omega
+Macromolecule #26: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 16.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: 70S ribosome without mRNA, tRNAs, or other factors bound. |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Details: as implemented in Relion 1.4 / Number images used: 15085 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-5my1: |