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Yorodumi- EMDB-9792: CryoEM structure of Escherichia coli sigmaE transcription initiat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9792 | |||||||||
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Title | CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA polymerase / Extra-Cytoplasmic Function sigma factors / sigmaE / transcription initiation / TRANSCRIPTION-DNA-RNA complex | |||||||||
Function / homology | Function and homology information sigma factor antagonist complex / response to osmotic stress / response to temperature stimulus / 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 ...sigma factor antagonist complex / response to osmotic stress / response to temperature stimulus / 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 / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.02 Å | |||||||||
Authors | Fang CL / Zhang Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2019 Title: Structures and mechanism of transcription initiation by bacterial ECF factors. Authors: Chengli Fang / Lingting Li / Liqiang Shen / Jing Shi / Sheng Wang / Yu Feng / Yu Zhang / Abstract: Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure ...Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE-the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation. | |||||||||
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_9792.map.gz | 9.7 MB | EMDB map data format | |
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Header (meta data) | emd-9792-v30.xml emd-9792.xml | 29.5 KB 29.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9792_fsc.xml | 7.6 KB | Display | FSC data file |
Images | emd_9792.png | 81 KB | ||
Filedesc metadata | emd-9792.cif.gz | 9.2 KB | ||
Others | emd_9792_half_map_1.map.gz emd_9792_half_map_2.map.gz | 27.3 MB 27.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9792 | HTTPS FTP |
-Validation report
Summary document | emd_9792_validation.pdf.gz | 811.3 KB | Display | EMDB validaton report |
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Full document | emd_9792_full_validation.pdf.gz | 810.9 KB | Display | |
Data in XML | emd_9792_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_9792_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9792 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9792 | HTTPS FTP |
-Related structure data
Related structure data | 6jbqMC 6jcxC 6jcyC M: atomic model generated by this map C: citing same article (ref.) |
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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_9792.map.gz / Format: CCP4 / Size: 35.3 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: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half2 unfil.mrc
File | emd_9792_half_map_1.map | ||||||||||||
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Annotation | half2_unfil.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half1 unfil.mrc
File | emd_9792_half_map_2.map | ||||||||||||
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Annotation | half1_unfil.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Escherichia coli sigmaE transcription initiation complex containi...
+Supramolecule #1: Escherichia coli sigmaE transcription initiation complex containi...
+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: ECF RNA polymerase sigma-E factor
+Macromolecule #6: DNA (48-MER)
+Macromolecule #7: DNA (48-MER)
+Macromolecule #8: RNA (5'-R(*CP*UP*CP*GP*A)-3')
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 15 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 120 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 282.65 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 2089 / Average exposure time: 8.0 sec. / Average electron dose: 1.665 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT | ||||||||
Output model | PDB-6jbq: |