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Yorodumi- EMDB-11419: E. coli 70S-RNAP expressome complex in collided state bound to NusG -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11419 | ||||||||||||||||||
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Title | E. coli 70S-RNAP expressome complex in collided state bound to NusG | ||||||||||||||||||
Map data | Collided E. coli expressome with intervening mRNA length 34 nucleotides bound to NusG: composite map | ||||||||||||||||||
Sample |
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Keywords | Transcription / Translation / Expressome / Ribosome / RNA polymerase / GENE REGULATION | ||||||||||||||||||
Function / homology | Function and homology information transcription elongation-coupled chromatin remodeling / 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 ...transcription elongation-coupled chromatin remodeling / 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 / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / nitrate assimilation / DNA-directed RNA polymerase complex / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / DNA-templated transcription initiation / response to reactive oxygen species / cell motility / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribonucleoside binding / mRNA 5'-UTR binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / response to heat / cytosolic small ribosomal subunit / protein-containing complex assembly / intracellular iron ion homeostasis / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / protein dimerization activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / 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 (E. coli) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Webster MW / Takacs M | ||||||||||||||||||
Funding support | France, 5 items
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Citation | Journal: Science / Year: 2020 Title: Structural basis of transcription-translation coupling and collision in bacteria. Authors: Michael William Webster / Maria Takacs / Chengjin Zhu / Vita Vidmar / Ayesha Eduljee / Mo'men Abdelkareem / Albert Weixlbaumer / Abstract: Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The ...Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo-electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study. | ||||||||||||||||||
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_11419.map.gz | 232.2 MB | EMDB map data format | |
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Header (meta data) | emd-11419-v30.xml emd-11419.xml | 111 KB 111 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11419_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_11419.png | 97.9 KB | ||
Filedesc metadata | emd-11419.cif.gz | 22 KB | ||
Others | emd_11419_additional_1.map.gz emd_11419_additional_2.map.gz emd_11419_additional_3.map.gz emd_11419_additional_4.map.gz emd_11419_additional_5.map.gz emd_11419_additional_6.map.gz emd_11419_additional_7.map.gz emd_11419_additional_8.map.gz emd_11419_half_map_1.map.gz emd_11419_half_map_2.map.gz | 516.6 MB 40.8 MB 219.5 MB 307.9 MB 517.5 MB 36.9 MB 31.2 MB 31.3 MB 254.4 MB 253.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11419 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11419 | HTTPS FTP |
-Validation report
Summary document | emd_11419_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_11419_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_11419_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | emd_11419_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11419 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11419 | HTTPS FTP |
-Related structure data
Related structure data | 6ztlMC 6ztjC 6ztmC 6ztnC 6ztoC 6ztpC 6zu1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10846 (Title: E. coli 70S-RNAP expressome complex in collided state (with NusG, 34nt intervening mRNA) [7712 multi-frame micrographs in TIFF format] Data size: 2.3 TB Data #1: E. coli 70S-RNAP expressome complex in collided state (with NusG, 34nt intervening mRNA) [7712 multi-frame micrographs in TIFF format] [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11419.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Collided E. coli expressome with intervening mRNA length 34 nucleotides bound to NusG: composite map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.075 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Additional map: Collided E. coli expressome with intervening mRNA length...
+Additional map: Collided E. coli expressome with intervening mRNA length...
+Additional map: Collided E. coli expressome with intervening mRNA length...
+Additional map: Collided E. coli expressome with intervening mRNA length...
+Additional map: Collided E. coli expressome with intervening mRNA length...
+Additional map: Collided E. coli expressome with intervening mRNA length...
+Additional map: Collided E. coli expressome with intervening mRNA length...
+Additional map: Collided E. coli expressome with intervening mRNA length...
+Half map: Collided E. coli expressome with intervening mRNA length...
+Half map: Collided E. coli expressome with intervening mRNA length...
-Sample components
+Entire : E. coli 70S-RNAP expressome complex in collided state bound to NusG
+Supramolecule #1: E. coli 70S-RNAP expressome complex in collided state bound to NusG
+Supramolecule #2: 70S ribosome within the collided E. coli expressome
+Supramolecule #3: DNA-directed RNA polymerase within the collided E. coli expressome
+Supramolecule #4: synthetic mRNA and template DNA
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #22: mRNA
+Macromolecule #23: tRNA(fmet) P-site
+Macromolecule #24: Phe-NH-tRNA(Phe) A-site
+Macromolecule #25: 23S ribosomal RNA
+Macromolecule #26: 5S ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+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 L6
+Macromolecule #32: 50S ribosomal protein L9
+Macromolecule #33: 50S ribosomal protein L13
+Macromolecule #34: 50S ribosomal protein L14
+Macromolecule #35: 50S ribosomal protein L15
+Macromolecule #36: 50S ribosomal protein L16
+Macromolecule #37: 50S ribosomal protein L17
+Macromolecule #38: 50S ribosomal protein L18
+Macromolecule #39: 50S ribosomal protein L19
+Macromolecule #40: 50S ribosomal protein L20
+Macromolecule #41: 50S ribosomal protein L21
+Macromolecule #42: 50S ribosomal protein L22
+Macromolecule #43: 50S ribosomal protein L23
+Macromolecule #44: 50S ribosomal protein L24
+Macromolecule #45: 50S ribosomal protein L25
+Macromolecule #46: 50S ribosomal protein L27
+Macromolecule #47: 50S ribosomal protein L28
+Macromolecule #48: 50S ribosomal protein L29
+Macromolecule #49: 50S ribosomal protein L30
+Macromolecule #50: 50S ribosomal protein L32
+Macromolecule #51: 50S ribosomal protein L33
+Macromolecule #52: 50S ribosomal protein L34
+Macromolecule #53: 50S ribosomal protein L35
+Macromolecule #54: 50S ribosomal protein L36
+Macromolecule #57: DNA-directed RNA polymerase subunit alpha
+Macromolecule #58: DNA-directed RNA polymerase subunit beta
+Macromolecule #59: DNA-directed RNA polymerase subunit beta'
+Macromolecule #60: DNA-directed RNA polymerase subunit omega
+Macromolecule #61: Transcription termination/antitermination protein NusG
+Macromolecule #55: Non-template DNA strand
+Macromolecule #56: Template DNA strand
+Macromolecule #62: MAGNESIUM ION
+Macromolecule #63: PHENYLALANINE
+Macromolecule #64: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7000000000000001 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient | ||||||
Output model | PDB-6ztl: |