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- PDB-7khi: Escherichia coli RNA polymerase and rrnBP1 promoter complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7khi | |||||||||
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Title | Escherichia coli RNA polymerase and rrnBP1 promoter complex with DksA/ppGpp | |||||||||
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![]() | TRANSCRIPTION/DNA / ![]() | |||||||||
Function / homology | ![]() sigma factor antagonist complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shin, Y. / Qayyum, M.Z. / Murakami, K.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of ribosomal RNA transcription regulation. Authors: Yeonoh Shin / M Zuhaib Qayyum / Danil Pupov / Daria Esyunina / Andrey Kulbachinskiy / Katsuhiko S Murakami / ![]() ![]() Abstract: Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. ...Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp. | |||||||||
History |
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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 | ![]() | 751 KB | Display | ![]() |
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PDB format | ![]() | 585.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 21881MC ![]() 7khbC ![]() 7khcC ![]() 7kheC 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: 26114.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: ![]() ![]() ![]() ![]() #2: Protein | | ![]() Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Production host: ![]() ![]() ![]() ![]() #3: Protein | | ![]() Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: rpoC, tabB, b3988, JW3951 / Production host: ![]() ![]() ![]() ![]() #4: Protein | | ![]() Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: rpoZ, b3649, JW3624 / Production host: ![]() ![]() ![]() ![]() |
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-Protein , 2 types, 2 molecules FM
#5: Protein | Mass: 70352.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Production host: ![]() ![]() ![]() |
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#8: Protein | Mass: 17554.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: dksA, b0145, JW0141 / Production host: ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules XY
#6: DNA chain | Mass: 10988.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#7: DNA chain | Mass: 8719.628 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 10 molecules ![](data/chem/img/1N7.gif)
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#9: Chemical | ChemComp-1N7 / ![]() #10: Chemical | ChemComp-MG / | #11: Chemical | #12: Chemical | ![]() |
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-Details
Has ligand of interest | Y |
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-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: Escherichia coli RNA polymerase and rrnBP1 promoter complex with DksA/ppGpp Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49995 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.28 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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