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- PDB-7c97: Cryo-EM structure of an Escherichia coli RNAP-promoter open compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c97 | ||||||
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Title | Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA | ||||||
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![]() | TRANSFERASE/DNA / Stringent starvation protein A / RNA polymerase / promoter escape / zinc binding domain / GENE REGULATION / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() response to stress / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / response to starvation / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly ...response to stress / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / response to starvation / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / glutathione transferase / bacterial-type flagellum-dependent cell motility / glutathione transferase activity / nitrate assimilation / glutathione metabolic process / 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 / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å | ||||||
![]() | Lin, W. / Feng, Y. | ||||||
![]() | ![]() Title: Structural basis for transcription inhibition by E. coli SspA. Authors: Fulin Wang / Jing Shi / Dingwei He / Bei Tong / Chao Zhang / Aijia Wen / Yu Zhang / Yu Feng / Wei Lin / ![]() Abstract: Stringent starvation protein A (SspA) is an RNA polymerase (RNAP)-associated protein involved in nucleotide metabolism, acid tolerance and virulence of bacteria. Despite extensive biochemical and ...Stringent starvation protein A (SspA) is an RNA polymerase (RNAP)-associated protein involved in nucleotide metabolism, acid tolerance and virulence of bacteria. Despite extensive biochemical and genetic analyses, the precise regulatory role of SspA in transcription is still unknown, in part, because of a lack of structural information for bacterial RNAP in complex with SspA. Here, we report a 3.68 Å cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA. Unexpectedly, the structure reveals that SspA binds to the E. coli σ70-RNAP holoenzyme as a homodimer, interacting with σ70 region 4 and the zinc binding domain of EcoRNAP β' subunit simultaneously. Results from fluorescent polarization assays indicate the specific interactions between SspA and σ70 region 4 confer its σ selectivity, thereby avoiding its interactions with σs or other alternative σ factors. In addition, results from in vitro transcription assays verify that SspA inhibits transcription probably through suppressing promoter escape. Together, the results here provide a foundation for understanding the unique physiological function of SspA in transcription regulation in bacteria. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 801.1 KB | Display | ![]() |
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PDB format | ![]() | 636.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30307MC ![]() 7chwC 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 chain , 2 types, 2 molecules HG
#1: DNA chain | Mass: 19671.666 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Nontemplate strand DNA of transcription initiation scaffold(RPo) Source: (synth.) ![]() ![]() |
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#8: DNA chain | Mass: 19159.285 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Template strand DNA of transcription initiation scaffold(RPo) Source: (synth.) ![]() ![]() |
-Protein , 2 types, 3 molecules IJF
#2: Protein | Mass: 24332.885 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: H4IXP2, UniProt: P0ACA3*PLUS, glutathione transferase #7: Protein | | Mass: 70352.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA-directed RNA polymerase subunit ... , 4 types, 6 molecules KABCDE
#3: Protein | Mass: 36558.680 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: F4VJT6, UniProt: P0A7Z4*PLUS, DNA-directed RNA polymerase #4: Protein | | Mass: 150804.922 Da / Num. of mol.: 1 / Mutation: D516V 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: ![]() ![]() #5: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: M9GTE2, UniProt: P0A8T7*PLUS, DNA-directed RNA polymerase #6: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: T9C803, UniProt: P0A800*PLUS, DNA-directed RNA polymerase |
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-Non-polymers , 2 types, 3 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#9: Chemical | ChemComp-MG / |
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#10: Chemical |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Escherichia coli RNAP-promoter open complex (RPo) with stringent starvation protein A(SspA) Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Molecular weight | Value: 0.55 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: BRIGHT FIELD |
Image recording | Electron dose: 59 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60145 / Symmetry type: POINT |