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Open data
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Basic information
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Title | EsN-dhsU36mm1 local map (map 2) | |||||||||
![]() | Raw map | |||||||||
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![]() | promoter-bound / initiation / TRANSCRIPTION | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Mueller AU / Chen J / Darst SA | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 32.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.1 KB 22.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 78.1 KB | ||
Masks | ![]() ![]() | 64 MB 64 MB | ![]() | |
Filedesc metadata | ![]() | 4.9 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 59.8 MB 2.4 MB 3 MB 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Raw map | ||||||||||||||||||||
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
-Mask #1
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Density Histograms |
-Mask #2
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Density Histograms |
-Additional map: B-factor sharpened map (-110.1)
File | emd_28794_additional_1.map | ||||||||||||
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Annotation | B-factor sharpened map (-110.1) | ||||||||||||
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Density Histograms |
-Additional map: Locally filtered map (blocfilt)
File | emd_28794_additional_2.map | ||||||||||||
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Annotation | Locally filtered map (blocfilt) | ||||||||||||
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-Additional map: Local resolution map (blocres)
File | emd_28794_additional_3.map | ||||||||||||
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Annotation | Local resolution map (blocres) | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_28794_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
-Half map: Half map B
File | emd_28794_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
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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: ![]() ![]() |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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. |
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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: ![]() |
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 |