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- EMDB-19795: RNA polymerase II early elongation complex bound to TFIIE and TFI... -

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Basic information

Entry
Database: EMDB / ID: EMD-19795
TitleRNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (global map)
Map datalocally filtered
Sample
  • Complex: RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a
    • Complex: RNA polymerase II
    • Complex: DNA and RNA
    • Cell: Transcription factor IIE and IIF
KeywordsRNA polymerase II / promoter escape / de novo transcription / TRANSCRIPTION
Biological speciesSus scrofa (pig) / unidentified adenovirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhan Y / Grabbe F / Oberbeckmann E / Dienemann C / Cramer P
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2024
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
DepositionMar 5, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19795.png

Downloads & links

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Map

FileDownload / File: emd_19795.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocally filtered
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0296
Minimum - Maximum-0.04382929 - 0.16907999
Average (Standard dev.)0.0008114574 (±0.0061454237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19795_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map

Fileemd_19795_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_19795_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA polymerase II early elongation complex bound to TFIIE and TFI...

EntireName: RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a
Components
  • Complex: RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a
    • Complex: RNA polymerase II
    • Complex: DNA and RNA
    • Cell: Transcription factor IIE and IIF

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Supramolecule #1: RNA polymerase II early elongation complex bound to TFIIE and TFI...

SupramoleculeName: RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: DNA and RNA

SupramoleculeName: DNA and RNA / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: unidentified adenovirus

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Supramolecule #4: Transcription factor IIE and IIF

SupramoleculeName: Transcription factor IIE and IIF / type: cell / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: EMDB MAP
EMDB ID:

12613

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65143
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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