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Yorodumi- EMDB-7059: The cryo-EM structure of a bacterial class I transcription activa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7059 | |||||||||
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Title | The cryo-EM structure of a bacterial class I transcription activation complex | |||||||||
Map data | Class I transcription activation complex | |||||||||
Sample |
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Keywords | transcription / RNA polymerase / catabolite activator protein / cAMP / TRANSCRIPTION-TRANSFERASE-DNA-RNA complex | |||||||||
Function / homology | Function and homology information sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-directed RNA polymerase complex / cAMP binding / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-directed RNA polymerase complex / cAMP binding / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli O157:H7 (bacteria) / Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria) / Escherichia coli O45:K1 (bacteria) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Liu B / Hong C | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2017 Title: Structural basis of bacterial transcription activation. Authors: Bin Liu / Chuan Hong / Rick K Huang / Zhiheng Yu / Thomas A Steitz / Abstract: In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic ...In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo-electron microscopy structure of an intact class I TAC containing a CAP dimer, a σ-RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide. The structure shows how CAP wraps the upstream DNA and how the interactions recruit RNAP. Our study provides a structural basis for understanding how activators activate transcription through the class I recruitment mechanism. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7059.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-7059-v30.xml emd-7059.xml | 29.9 KB 29.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7059_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_7059.png | 76.8 KB | ||
Filedesc metadata | emd-7059.cif.gz | 9.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7059 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7059 | HTTPS FTP |
-Validation report
Summary document | emd_7059_validation.pdf.gz | 449.8 KB | Display | EMDB validaton report |
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Full document | emd_7059_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | emd_7059_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | emd_7059_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7059 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7059 | HTTPS FTP |
-Related structure data
Related structure data | 6b6hMC 7060C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7059.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Class I transcription activation complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : The complex of class-I bacterial transcription activation complex
+Supramolecule #1: The complex of class-I bacterial transcription activation 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 #6: cAMP-activated global transcriptional regulator CRP
+Macromolecule #7: DNA-directed RNA polymerase subunit alpha
+Macromolecule #8: SYNTHETIC NONTEMPLATE STRAND DNA (88-MER)
+Macromolecule #9: SYNTHETIC TEMPLATE STRAND DNA (88-MER)
+Macromolecule #10: NASCENT RNA 3-MER
+Macromolecule #11: ZINC ION
+Macromolecule #12: MAGNESIUM ION
+Macromolecule #13: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: 20 mM TRIS pH 7.5, 50 mM sodium chloride, 0.1mM EDTA, 5 mM MgCl2, 5 mM DTT | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blotting. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Details | Cs corrector |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2382 / Average exposure time: 0.25 sec. / Average electron dose: 1.37 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |
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Output model | PDB-6b6h: |