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- EMDB-53116: CryoEM structure of transcribing RNA polymerase II elongation com... -

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Basic information

Entry
Database: EMDB / ID: EMD-53116
TitleCryoEM structure of transcribing RNA polymerase II elongation complex_Composite map
Map dataCryoEM structure of transcribing RNA polymerase II elongation complex_Composite map
Sample
  • Complex: Yeast RNA Polymerase II elongation complex
KeywordsCryoEM / RNA / Polymerase / Transcription
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsLi Q / Yi G / Zhang P / Wang D
Funding support United Kingdom, United States, 6 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102362 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM148476 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147652 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI170791-7522 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)CA280467 United States
CitationJournal: To Be Published
Title: CryoEM structure of transcribing RNA polymerase II elongation complex
Authors: Li Q / Yi G / Zhang P / Wang D
History
DepositionMar 11, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53116.png

Downloads & links

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Map

FileDownload / File: emd_53116.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of transcribing RNA polymerase II elongation complex_Composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 420 pix.
= 348.18 Å		0.83 Å/pix.
x 420 pix.
= 348.18 Å		0.83 Å/pix.
x 420 pix.
= 348.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum0.0 - 1.9859893
Average (Standard dev.)0.0024444303 (±0.031935655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 348.18 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yeast RNA Polymerase II elongation complex

EntireName: Yeast RNA Polymerase II elongation complex
Components
  • Complex: Yeast RNA Polymerase II elongation complex

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Supramolecule #1: Yeast RNA Polymerase II elongation complex

SupramoleculeName: Yeast RNA Polymerase II elongation complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 0.513 kDa/nm

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2e2h


Details: 2E2H and 8U9R
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 692163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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