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Yorodumi- EMDB-32324: Cryo-EM structure of SoxS-dependent transcription activation comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32324 | |||||||||
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Title | Cryo-EM structure of SoxS-dependent transcription activation complex with fpr promoter DNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | bacterial RNA polymerase / TRANSCRIPTION-DNA COMPLEX | |||||||||
Function / homology | Function and homology information bacterial-type RNA polymerase holo enzyme binding / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly ...bacterial-type RNA polymerase holo enzyme binding / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / 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 / cis-regulatory region sequence-specific DNA binding / 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 / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Lin W / Feng Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Structural basis of three different transcription activation strategies adopted by a single regulator SoxS. Authors: Jing Shi / Lu Wang / Aijia Wen / Fulin Wang / Yuqiong Zhang / Libing Yu / Fangfang Li / Yuanling Jin / Zhenzhen Feng / Jiacong Li / Yujiao Yang / Fei Gao / Yu Zhang / Yu Feng / Shuang Wang / ...Authors: Jing Shi / Lu Wang / Aijia Wen / Fulin Wang / Yuqiong Zhang / Libing Yu / Fangfang Li / Yuanling Jin / Zhenzhen Feng / Jiacong Li / Yujiao Yang / Fei Gao / Yu Zhang / Yu Feng / Shuang Wang / Wei Zhao / Wei Lin / Abstract: Transcription activation is established through extensive protein-protein and protein-DNA interactions that allow an activator to engage and remodel RNA polymerase. SoxS, a global transcription ...Transcription activation is established through extensive protein-protein and protein-DNA interactions that allow an activator to engage and remodel RNA polymerase. SoxS, a global transcription activator, diversely regulates subsets of stress response genes with different promoters, but the detailed SoxS-dependent transcription initiation mechanisms remain obscure. Here, we report cryo-EM structures of three SoxS-dependent transcription activation complexes (SoxS-TACI, SoxS-TACII and SoxS-TACIII) comprising of Escherichia coli RNA polymerase (RNAP), SoxS protein and three representative classes of SoxS-regulated promoters. The structures reveal that SoxS monomer orchestrates transcription initiation through specific interactions with the promoter DNA and different conserved domains of RNAP. In particular, SoxS is positioned in the opposite orientation in SoxS-TACIII to that in SoxS-TACI and SoxS-TACII, unveiling a novel mode of transcription activation. Strikingly, two universally conserved C-terminal domains of alpha subunit (αCTD) of RNAP associate with each other, bridging SoxS and region 4 of σ70. We show that SoxS interacts with RNAP directly and independently from DNA, remodeling the enzyme to activate transcription from cognate SoxS promoters while repressing transcription from UP-element containing promoters. Our data provide a comprehensive summary of SoxS-dependent promoter architectures and offer new insights into the αCTD contribution to transcription control in bacteria. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32324.map.gz | 37.9 MB | EMDB map data format | |
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Header (meta data) | emd-32324-v30.xml emd-32324.xml | 23.2 KB 23.2 KB | Display Display | EMDB header |
Images | emd_32324.png | 72.6 KB | ||
Filedesc metadata | emd-32324.cif.gz | 8.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32324 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32324 | HTTPS FTP |
-Validation report
Summary document | emd_32324_validation.pdf.gz | 723.2 KB | Display | EMDB validaton report |
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Full document | emd_32324_full_validation.pdf.gz | 722.8 KB | Display | |
Data in XML | emd_32324_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_32324_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32324 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32324 | HTTPS FTP |
-Related structure data
Related structure data | 7w5yMC 7w5wC 7w5xC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32324.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.307 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : SoxS-dependent transcription activation complex with fpr promoter DNA
+Supramolecule #1: SoxS-dependent transcription activation complex with fpr promoter DNA
+Supramolecule #2: DNA-directed RNA polymerase subunits
+Supramolecule #3: DNA
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: RNA polymerase sigma factor RpoD
+Macromolecule #8: Regulatory protein SoxS
+Macromolecule #6: fpr promoter DNA forward strand
+Macromolecule #7: fpr promoter DNA reverse strand
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74601 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |