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Yorodumi- EMDB-14171: CryoEM structure of bacterial transcription intermediate complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14171 | |||||||||
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Title | CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF | |||||||||
Map data | Local filtered map | |||||||||
Sample |
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Function / homology | Function and homology information RNA polymerase complex / DNA-binding transcription activator activity / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...RNA polymerase complex / DNA-binding transcription activator activity / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / bacterial-type flagellum-dependent cell motility / nitrate assimilation / nucleotidyltransferase activity / transcription elongation factor complex / DNA-directed RNA polymerase 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 / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Klebsiella pneumoniae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ye FZ / Zhang XD | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Mechanisms of DNA opening revealed in AAA+ transcription complex structures. Authors: Fuzhou Ye / Forson Gao / Xiaojiao Liu / Martin Buck / Xiaodong Zhang / Abstract: Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter ...Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo-electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ inhibition while helping to open up DNA, using σ amino-terminal peptide as a pry bar. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14171.map.gz | 49.6 MB | EMDB map data format | |
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Header (meta data) | emd-14171-v30.xml emd-14171.xml | 30.5 KB 30.5 KB | Display Display | EMDB header |
Images | emd_14171.png | 168.6 KB | ||
Others | emd_14171_additional_1.map.gz emd_14171_additional_2.map.gz | 49.3 MB 45.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14171 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14171 | HTTPS FTP |
-Related structure data
Related structure data | 7qv9MC 7qwpC 7qxiC 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_14171.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Local filtered map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Focus refinement map
File | emd_14171_additional_1.map | ||||||||||||
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Annotation | Focus refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focus refinement map
File | emd_14171_additional_2.map | ||||||||||||
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Annotation | Focus refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Bacterial transcription intermediate complex mediated by PspF act...
+Supramolecule #1: Bacterial transcription intermediate complex mediated by PspF act...
+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 #7: Transcription activator PspF
+Macromolecule #8: RNA polymerase sigma-54 factor
+Macromolecule #5: Non-template promoter DNA
+Macromolecule #6: Template promoter DNA
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #10: ALUMINUM FLUORIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.5 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 14780 / Average exposure time: 4.1 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 2000000 |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. RELION 3.1) |
Final 3D classification | Number classes: 3 / Software - Name: RELION (ver. RELION 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. RELION 3.1) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. RELION 3.1) / Number images used: 33285 |