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Open data
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Basic information
Entry | Database: PDB / ID: 3lu0 | ||||||
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Title | Molecular model of Escherichia coli core RNA polymerase | ||||||
![]() | (DNA-directed RNA polymerase subunit ...![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Darst, S.A. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 565.9 KB | Display | ![]() |
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PDB format | ![]() | 436.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5169MC ![]() 3ltiC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | ![]() Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | | ![]() Mass: 150804.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: b3987, groN, JW3950, nitB, rif, ron, rpoB, rpoC, stl, stv, tabD Production host: ![]() ![]() ![]() ![]() #3: Protein | | ![]() Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #4: Protein | | ![]() Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 2 types, 3 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
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#5: Chemical | ChemComp-MG / |
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#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: E. coli RNA polymerase / Type: COMPLEX |
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Buffer solution | Name: Tris-HCl![]() |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: single-tilt / Temperature: 80 K |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 48 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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Symmetry | Point symmetry![]() | |||||||||||||||
3D reconstruction![]() | Resolution: 11.2 Å / Num. of particles: 42000 / Nominal pixel size: 2.8 Å / Symmetry type: POINT | |||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--local refinement, flexible fitting | |||||||||||||||
Refinement step | Cycle: LAST
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