+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28797 | |||||||||
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Title | EsN-dhsU36mm1 composite map | |||||||||
Map data | Composite of raw full and local maps | |||||||||
Sample |
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Keywords | promoter-bound / initiation / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information arginine metabolic process / DNA-binding transcription activator activity / 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 ...arginine metabolic process / DNA-binding transcription activator activity / 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 / nucleotidyltransferase activity / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / protein-DNA complex / 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 / transcription cis-regulatory region binding / response to antibiotic / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Aquifex aeolicus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Mueller AU / Chen J / Darst SA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: A general mechanism for transcription bubble nucleation in bacteria. Authors: Andreas U Mueller / James Chen / Mengyu Wu / Courtney Chiu / B Tracy Nixon / Elizabeth A Campbell / Seth A Darst / Abstract: Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ, nucleates DNA melting via recognition of conserved bases ...Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ, nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ. By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σ-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σ, like σ, captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28797.map.gz | 30.3 MB | EMDB map data format | |
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Header (meta data) | emd-28797-v30.xml emd-28797.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
Images | emd_28797.png | 122.3 KB | ||
Filedesc metadata | emd-28797.cif.gz | 4.6 KB | ||
Others | emd_28797_additional_1.map.gz emd_28797_additional_2.map.gz | 9 MB 57.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28797 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28797 | HTTPS FTP |
-Validation report
Summary document | emd_28797_validation.pdf.gz | 480.6 KB | Display | EMDB validaton report |
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Full document | emd_28797_full_validation.pdf.gz | 480.1 KB | Display | |
Data in XML | emd_28797_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_28797_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28797 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28797 | HTTPS FTP |
-Related structure data
Related structure data | 8f1iMC 8f1jC 8f1kC C: citing same article (ref.) M: atomic model generated by this map |
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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_28797.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite of raw full and local maps | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.083 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Locally filtered composite map (blocfilt)
File | emd_28797_additional_1.map | ||||||||||||
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Annotation | Locally filtered composite map (blocfilt) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite of B-factor sharpened full and local maps
File | emd_28797_additional_2.map | ||||||||||||
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Annotation | Composite of B-factor sharpened full and local maps | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : EsN-dhsU36mm1
Entire | Name: EsN-dhsU36mm1 |
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Components |
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-Supramolecule #1: EsN-dhsU36mm1
Supramolecule | Name: EsN-dhsU36mm1 / type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: RNA polymerase complex
Supramolecule | Name: RNA polymerase complex / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) / Synthetically produced: Yes |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: Octyl beta-D-glucopyranoside (beta-OG) was added to the sample to 0.1%w/v final concentration (from 10x stock) just prior to plunge vitrification. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 12294 / Average exposure time: 2.0 sec. / Average electron dose: 51.0 e/Å2 Details: dose-fractionation with 0.05 seconds per frame (=40 frames) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: ab initio generated map |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Software - details: phenix.combine_focused_maps Details: Particle numbers and FSC resolution estimate of the full map given Number images used: 602287 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |