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Basic information

Entry
Database: EMDB / ID: EMD-54677
TitleCryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class A (frame1)
Map data
Sample
  • Complex: Yeast RNA polymerase II elongation complex
KeywordsCryoEM / RNA Polymerase / Transcription
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsYi G / Li Q / Wang D / Zhang P
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: Biorxiv / Year: 2026
Title: Structural Dynamics of RNA Polymerase II During Nucleotide Addition Cycle.
Authors: Yi G / Li Q / Holmberg H / Li S / Clare DK / Wang D / Zhang P
History
DepositionAug 6, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54677.png

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Map

FileReleased
Voxel sizeX=Y=Z: 1.0881 Å
Density
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.43664074 - 0.8318362
Average (Standard dev.)0.00007607775 (±0.02829406)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 348.192 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: 513 KDa

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: PHENIX, UCSF Chimera, UCSF ChimeraX) / Number images used: 65010
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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