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- EMDB-20460: Escherichia coli RNA polymerase closed complex (TRPc) with TraR a... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20460 | |||||||||
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Title | Escherichia coli RNA polymerase closed complex (TRPc) with TraR and rpsT P2 promoter | |||||||||
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![]() | TRANSCRIPTION / transcription-dna complex | |||||||||
Function / homology | ![]() positive regulation of secondary metabolite biosynthetic process / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / 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 ...positive regulation of secondary metabolite biosynthetic process / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / 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 / DNA-directed RNA polymerase complex / 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 / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Chen J / Chiu CE | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Stepwise Promoter Melting by Bacterial RNA Polymerase. Authors: James Chen / Courtney Chiu / Saumya Gopalkrishnan / Albert Y Chen / Paul Dominic B Olinares / Ruth M Saecker / Jared T Winkelman / Michael F Maloney / Brian T Chait / Wilma Ross / Richard L ...Authors: James Chen / Courtney Chiu / Saumya Gopalkrishnan / Albert Y Chen / Paul Dominic B Olinares / Ruth M Saecker / Jared T Winkelman / Michael F Maloney / Brian T Chait / Wilma Ross / Richard L Gourse / Elizabeth A Campbell / Seth A Darst / ![]() Abstract: Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into ...Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 60 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.8 KB 21.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 52.5 KB | ||
Filedesc metadata | ![]() | 8.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6psqMC ![]() 6psrC ![]() 6pssC ![]() 6pstC ![]() 6psuC ![]() 6psvC ![]() 6pswC M: atomic model generated by this map C: citing same article ( |
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Similar 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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Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Escherichia coli sigma70-holoenzyme bound to TraR and Wildtype rp...
+Supramolecule #1: Escherichia coli sigma70-holoenzyme bound to TraR and Wildtype rp...
+Macromolecule #1: DNA-directed RNA polymerase subunit beta'
+Macromolecule #2: Protein TraR
+Macromolecule #3: DNA-directed RNA polymerase subunit alpha
+Macromolecule #4: DNA-directed RNA polymerase subunit beta
+Macromolecule #5: DNA-directed RNA polymerase subunit omega
+Macromolecule #6: RNA polymerase sigma factor RpoD
+Macromolecule #7: DNA (85-MER)
+Macromolecule #8: DNA (85-MER)
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC ION
+Macromolecule #11: CHAPSO
-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 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |