+
Open data
-
Basic information
Entry | Database: PDB / ID: 6c9y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of E. coli RNAP sigma70 holoenzyme | |||||||||
![]() |
| |||||||||
![]() | TRANSCRIPTION / Escherichia coli / RNA polymerase | |||||||||
Function / homology | ![]() sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / 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 / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å | |||||||||
![]() | Narayanan, A. / Vago, F. / Li, K. / Qayyum, M.Z. / Yenool, D. / Jiang, W. / Murakami, K.S. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo-EM structure of σ RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation. Authors: Anoop Narayanan / Frank S Vago / Kunpeng Li / M Zuhaib Qayyum / Dinesh Yernool / Wen Jiang / Katsuhiko S Murakami / ![]() Abstract: First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In , a primary σ factor forms the RNAP ...First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In , a primary σ factor forms the RNAP holoenzyme to express housekeeping genes. The σ contains a large insertion between the conserved regions 1.2 and 2.1, the σ non-conserved region (σ), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the RNAP σ holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between the σ and promoter DNA just upstream of the -10 element, which was not observed in a previously determined RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of the σ and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σ and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 653.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 527.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7438MC ![]() 7439C ![]() 6ca0C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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.) ![]() ![]() 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: ![]() ![]() |
---|
-Protein , 1 types, 1 molecules F
#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: ![]() ![]() |
---|
-Non-polymers , 2 types, 3 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#6: Chemical | ChemComp-MG / |
---|---|
#7: Chemical |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: DNA-directed RNA polymerase / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96067 / Symmetry type: POINT |