+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7439 | |||||||||
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Title | Cryo-EM structure of E. coli RNAP sigma70 open complex | |||||||||
Map data | Cryo-EM structure of E. coli RNAP sigma70 open complex | |||||||||
Sample |
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Keywords | Escherichia coli / RNA polymerase / TRANSCRIPTION / transcription-dna complex | |||||||||
Function / homology | Function and homology information sigma factor antagonist complex / 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 ...sigma factor antagonist complex / 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 / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.75 Å | |||||||||
Authors | Narayanan A / Vago F | |||||||||
Funding support | United States, 2 items
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Citation | Journal: J Biol Chem / Year: 2018 Title: Cryo-EM structure of σ RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation. Authors: Anoop Narayanan / Frank S Vago / Kunpeng Li / M Zuhaib Qayyum / Dinesh Yernool / Wen Jiang / Katsuhiko S Murakami / Abstract: First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In , a primary σ factor forms the RNAP ...First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In , a primary σ factor forms the RNAP holoenzyme to express housekeeping genes. The σ contains a large insertion between the conserved regions 1.2 and 2.1, the σ non-conserved region (σ), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the RNAP σ holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between the σ and promoter DNA just upstream of the -10 element, which was not observed in a previously determined RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of the σ and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σ and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor. | |||||||||
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_7439.map.gz | 48.3 MB | EMDB map data format | |
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Header (meta data) | emd-7439-v30.xml emd-7439.xml | 22 KB 22 KB | Display Display | EMDB header |
Images | emd_7439.png | 49.5 KB | ||
Filedesc metadata | emd-7439.cif.gz | 8.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7439 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7439 | HTTPS FTP |
-Validation report
Summary document | emd_7439_validation.pdf.gz | 492.1 KB | Display | EMDB validaton report |
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Full document | emd_7439_full_validation.pdf.gz | 491.7 KB | Display | |
Data in XML | emd_7439_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_7439_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7439 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7439 | HTTPS FTP |
-Related structure data
Related structure data | 6ca0MC 7438C 6c9yC 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_7439.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of E. coli RNAP sigma70 open complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.316 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 : DNA-directed RNA polymerase open complex
+Supramolecule #1: DNA-directed RNA polymerase open 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: DNA (45-MER)
+Macromolecule #7: DNA (35-MER)
+Macromolecule #8: DNA (5'-D(P*TP*CP*TP*GP*AP*CP*GP*CP*GP*GP*C)-3')
+Macromolecule #9: DNA (5'-D(P*GP*CP*CP*GP*CP*GP*TP*CP*AP*GP*A)-3')
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96067 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |