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- EMDB-5169: Single-particle cryo-EM reconstruction of E. coli core RNA polymerase -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5169 | |||||||||
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Title | Single-particle cryo-EM reconstruction of E. coli core RNA polymerase | |||||||||
![]() | Single-particle cryo-EM reconstruction of E. coli core RNA polymerase | |||||||||
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![]() | E coli / ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Opalka N / Brown J / Lane WJ / Twist KF / Landick R / Asturias FJ / Darst SA | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.7 KB 9.7 KB | Display Display | ![]() |
Images | ![]() | 138.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lu0MC ![]() 3ltiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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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 | divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ... divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kGO3A00708 60ampajax1 classpoptr giGO007086 0ispandiv |
Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder: single-tilt / Specimen holder model: GATAN LIQUID NITROGEN |
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 |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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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 |