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Yorodumi- EMDB-5169: Single-particle cryo-EM reconstruction of E. coli core RNA polymerase -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5169 | |||||||||
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Title | Single-particle cryo-EM reconstruction of E. coli core RNA polymerase | |||||||||
Map data | Single-particle cryo-EM reconstruction of E. coli core RNA polymerase | |||||||||
Sample |
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Keywords | E coli / polymerase / transcription | |||||||||
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 / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation ...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 / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.0 Å | |||||||||
Authors | Opalka N / Brown J / Lane WJ / Twist KF / Landick R / Asturias FJ / Darst SA | |||||||||
Citation | Journal: PLoS Biol / Year: 2010 Title: Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. Authors: Natacha Opalka / Jesse Brown / William J Lane / Kelly-Anne F Twist / Robert Landick / Francisco J Asturias / Seth A Darst / Abstract: The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the ...The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program. | |||||||||
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_5169.map.gz | 2.6 MB | EMDB map data format | |
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Header (meta data) | emd-5169-v30.xml emd-5169.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_5169_1.jpg | 138.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5169 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5169 | HTTPS FTP |
-Validation report
Summary document | emd_5169_validation.pdf.gz | 300 KB | Display | EMDB validaton report |
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Full document | emd_5169_full_validation.pdf.gz | 299.6 KB | Display | |
Data in XML | emd_5169_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5169 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5169 | HTTPS FTP |
-Related structure data
Related structure data | 3lu0MC 3ltiC 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_5169.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single-particle cryo-EM reconstruction of E. coli core RNA polymerase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 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 : E. coli RNA polymerase
Entire | Name: E. coli RNA polymerase |
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Components |
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-Supramolecule #1000: E. coli RNA polymerase
Supramolecule | Name: E. coli RNA polymerase / type: sample / ID: 1000 / Number unique components: 4 |
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Molecular weight | Experimental: 380 KDa / Theoretical: 378.8 KDa / Method: primary sequence |
-Supramolecule #1: RNA polymerase
Supramolecule | Name: RNA polymerase / type: organelle_or_cellular_component / ID: 1 / Name.synonym: bacterial RNA polymerase / Recombinant expression: Yes |
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Ref GO | 0: GO:0070860 |
Source (natural) | Organism: Escherichia coli (E. coli) / synonym: E coli / Cell: E coli |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 Details: 10 mM Tris-HCl, pH 8, 0.2 M NaCl, 0.1 mM EDTA, 5 mM DTT |
Grid | Details: 300 mesh Cu/Rd |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: custom plunger |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 103 K / Max: 110 K / Average: 109 K |
Alignment procedure | Legacy - Astigmatism: FT |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 2.8 µm / Number real images: 48 / Average electron dose: 10 e/Å2 / Bits/pixel: 10 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: single-tilt / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: OTHER / Software - Name: SPIDER AND SPARX / Number images used: 42000 |