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Yorodumi- EMDB-30307: Cryo-EM structure of an Escherichia coli RNAP-promoter open compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30307 | |||||||||
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Title | Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Stringent starvation protein A / RNA polymerase / promoter escape / zinc binding domain / GENE REGULATION / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information 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 / bacterial-type flagellum assembly / sigma factor activity / glutathione transferase ...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 / bacterial-type flagellum assembly / sigma factor activity / 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 / cell motility / DNA-templated transcription initiation / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
Authors | Lin W / Feng Y | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2020 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30307.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-30307-v30.xml emd-30307.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
Images | emd_30307.png | 123.6 KB | ||
Filedesc metadata | emd-30307.cif.gz | 8.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30307 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30307 | HTTPS FTP |
-Related structure data
Related structure data | 7c97MC 7chwC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30307.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.307 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Escherichia coli RNAP-promoter open complex (RPo) with stringent ...
+Supramolecule #1: Escherichia coli RNAP-promoter open complex (RPo) with stringent ...
+Macromolecule #1: DNA (63-mer)
+Macromolecule #8: DNA (63-mer)
+Macromolecule #2: Stringent starvation protein A
+Macromolecule #3: DNA-directed RNA polymerase subunit alpha
+Macromolecule #4: DNA-directed RNA polymerase subunit beta
+Macromolecule #5: DNA-directed RNA polymerase subunit beta'
+Macromolecule #6: DNA-directed RNA polymerase subunit omega
+Macromolecule #7: RNA polymerase sigma factor RpoD
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 59.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 60145 |