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- EMDB-19725: RNA polymerase II early elongation complex bound to TFIIE, TFIIF ... -
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Open data
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Basic information
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Title | RNA polymerase II early elongation complex bound to TFIIE, TFIIF and TFIIH - state b | |||||||||
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![]() | RNA polymerase II / promoter escape / de novo transcription / TRANSCRIPTION | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.2 Å | |||||||||
![]() | Zhan Y / Grabbe F / Oberbeckmann E / Dienemann C / Cramer P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Three-step mechanism of promoter escape by RNA polymerase II. Authors: Yumeng Zhan / Frauke Grabbe / Elisa Oberbeckmann / Christian Dienemann / Patrick Cramer / ![]() Abstract: The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how ...The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 140.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
Images | ![]() | 86.9 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 3.7 KB | ||
Others | ![]() ![]() | 194.7 MB 194.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19725_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : mammalian RNA polymerase II general transcription factor IIA gene...
Entire | Name: mammalian RNA polymerase II general transcription factor IIA general transcription factor IIB general transcription factor IIE general transcription factor IIF general transcription factor IIH ...Name: mammalian RNA polymerase II general transcription factor IIA general transcription factor IIB general transcription factor IIE general transcription factor IIF general transcription factor IIH TATA-box binding protein DNA |
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Components |
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-Supramolecule #1: mammalian RNA polymerase II general transcription factor IIA gene...
Supramolecule | Name: mammalian RNA polymerase II general transcription factor IIA general transcription factor IIB general transcription factor IIE general transcription factor IIF general transcription factor IIH ...Name: mammalian RNA polymerase II general transcription factor IIA general transcription factor IIB general transcription factor IIE general transcription factor IIF general transcription factor IIH TATA-box binding protein DNA type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: RNA polymerase II
Supramolecule | Name: RNA polymerase II / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: ![]() ![]() |
-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: 7.5 |
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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 K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8814 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |