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Yorodumi- EMDB-29423: Structure of Escherichia coli CedA in complex with transcription ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29423 | ||||||||||||
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Title | Structure of Escherichia coli CedA in complex with transcription initiation complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Escherichia coli / CedA / initiation complex / TRANSCRIPTION / TRANSFERASE-DNA complex | ||||||||||||
Function / homology | Function and homology information cell cycle / 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 ...cell cycle / 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 / 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 / cell division / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.76 Å | ||||||||||||
Authors | Liu M / Vassyliev N / Nudler E | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: General transcription factor from Escherichia coli with a distinct mechanism of action. Authors: Nikita Vasilyev / Mengjie M J Liu / Vitaly Epshtein / Ilya Shamovsky / Evgeny Nudler / Abstract: Gene expression in Escherichia coli is controlled by well-established mechanisms that activate or repress transcription. Here, we identify CedA as an unconventional transcription factor specifically ...Gene expression in Escherichia coli is controlled by well-established mechanisms that activate or repress transcription. Here, we identify CedA as an unconventional transcription factor specifically associated with the RNA polymerase (RNAP) σ holoenzyme. Structural and biochemical analysis of CedA bound to RNAP reveal that it bridges distant domains of β and σ subunits to stabilize an open-promoter complex. CedA does so without contacting DNA. We further show that cedA is strongly induced in response to amino acid starvation, oxidative stress and aminoglycosides. CedA provides a basal level of tolerance to these clinically relevant antibiotics, as well as to rifampicin and peroxide. Finally, we show that CedA modulates transcription of hundreds of bacterial genes, which explains its pleotropic effect on cell physiology and pathogenesis. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29423.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-29423-v30.xml emd-29423.xml | 27.8 KB 27.8 KB | Display Display | EMDB header |
Images | emd_29423.png | 193.6 KB | ||
Filedesc metadata | emd-29423.cif.gz | 9.2 KB | ||
Others | emd_29423_half_map_1.map.gz emd_29423_half_map_2.map.gz | 165.2 MB 165.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29423 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29423 | HTTPS FTP |
-Validation report
Summary document | emd_29423_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29423_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29423_validation.xml.gz | 15 KB | Display | |
Data in CIF | emd_29423_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29423 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29423 | HTTPS FTP |
-Related structure data
Related structure data | 8ftdMC 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_29423.map.gz / Format: CCP4 / Size: 178 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: 0.852 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_29423_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29423_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Escherichia coli CedA in complex with initiation complex
+Supramolecule #1: Escherichia coli CedA in complex with initiation complex
+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: Cell division activator CedA
+Macromolecule #6: Transcription Unit ssrA Promoter Non-template DNA
+Macromolecule #7: Transcription Unit ssrA Promoter Template DNA
+Macromolecule #9: CHAPSO
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 15mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 1.416 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
-Image processing
Startup model | Type of model: OTHER Details: The initial model was created in-house using CryoSPARC |
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Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 177841 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD Details: The initial model was created in-house using CryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Details: Final refinement was performed using CryoSPARC |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-8ftd: |