+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10547 | |||||||||
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Title | bacterial RNA polymerase rrnTAC (global state) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information glycerol-2-phosphatase activity / : / lithium ion binding / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / DNA-templated transcription elongation / inositol metabolic process / bacterial-type RNA polymerase core enzyme binding ...glycerol-2-phosphatase activity / : / lithium ion binding / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / DNA-templated transcription elongation / inositol metabolic process / bacterial-type RNA polymerase core enzyme binding / rRNA primary transcript 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 / transcription antitermination factor activity, RNA binding / phosphatidylinositol phosphate biosynthetic process / bacterial-type flagellum-dependent cell motility / nitrate assimilation / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / transcription elongation factor complex / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / maintenance of translational fidelity / DNA-templated transcription termination / DNA-templated transcription initiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribonucleoside binding / ribosomal small subunit assembly / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytosolic small ribosomal subunit / ribosome biogenesis / protein complex oligomerization / cytoplasmic translation / small ribosomal subunit / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / tRNA binding / rRNA binding / protein dimerization activity / ribosome / structural constituent of ribosome / translation / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / signal transduction / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Hilal T / Huang Y / Wahl MC | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Mol Cell / Year: 2020 Title: Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis. Authors: Yong-Heng Huang / Tarek Hilal / Bernhard Loll / Jörg Bürger / Thorsten Mielke / Christoph Böttcher / Nelly Said / Markus C Wahl / Abstract: Bacterial ribosomal RNAs are synthesized by a dedicated, conserved transcription-elongation complex that transcribes at high rates, shields RNA polymerase from premature termination, and supports co- ...Bacterial ribosomal RNAs are synthesized by a dedicated, conserved transcription-elongation complex that transcribes at high rates, shields RNA polymerase from premature termination, and supports co-transcriptional RNA folding, modification, processing, and ribosomal subunit assembly by presently unknown mechanisms. We have determined cryo-electron microscopy structures of complete Escherichia coli ribosomal RNA transcription elongation complexes, comprising RNA polymerase; DNA; RNA bearing an N-utilization-site-like anti-termination element; Nus factors A, B, E, and G; inositol mono-phosphatase SuhB; and ribosomal protein S4. Our structures and structure-informed functional analyses show that fast transcription and anti-termination involve suppression of NusA-stabilized pausing, enhancement of NusG-mediated anti-backtracking, sequestration of the NusG C-terminal domain from termination factor ρ, and the ρ blockade. Strikingly, the factors form a composite RNA chaperone around the RNA polymerase RNA-exit tunnel, which supports co-transcriptional RNA folding and annealing of distal RNA regions. Our work reveals a polymerase/chaperone machine required for biosynthesis of functional ribosomes. | |||||||||
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_10547.map.gz | 95.3 MB | EMDB map data format | |
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Header (meta data) | emd-10547-v30.xml emd-10547.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10547_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_10547.png | 52.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10547 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10547 | HTTPS FTP |
-Related 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_10547.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.24 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 : bacterial rRNA transcription anti-termination complex
Entire | Name: bacterial rRNA transcription anti-termination complex |
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Components |
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-Supramolecule #1: bacterial rRNA transcription anti-termination complex
Supramolecule | Name: bacterial rRNA transcription anti-termination complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 633 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 10 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 31000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-50 / Number real images: 2706 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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