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- EMDB-54680: CryoEM map of Yeast RNA polymerase II elongation complex with ATP... -

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Entry
Database: EMDB / ID: EMD-54680
TitleCryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class D (frame8)
Map dataCryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class D (frame8)
Sample
  • Complex: Yeast RNA polymerase II elongation complex
KeywordsCryoEM / RNA Polymerase / Transcription
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 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: Gangshun Yi / Qingrong Li / Hannah Holmberg / Shisheng Li / Daniel K Clare / Dong Wang / Peijun Zhang
Abstract: RNA polymerase II (RNAPII) drives gene expression through iterative nucleotide addition cycles (NACs) comprising translocation, substrate binding, and catalysis. The lack of pre-catalysis and post- ...RNA polymerase II (RNAPII) drives gene expression through iterative nucleotide addition cycles (NACs) comprising translocation, substrate binding, and catalysis. The lack of pre-catalysis and post-catalysis intermediates has precluded a complete mechanistic understanding of the NAC. Here we present 43 cryo-EM structures capturing distinct stages of the RNAPII elongation complex (EC) NAC, including previously intractable transition intermediates. We establish a continuous spectrum of RNAPII EC structural dynamics during the NAC, which can be divided into two coordinated phases: a substrate-induced EC tightening phase and a post-catalysis EC relaxation phase. For the substrate-induced EC tightening phase, the substrate binding initiates allosteric conformational changes across the entire RNAPII EC, including TL folding, funnel closure, clamp closure, transcription bubble ordering, and precise alignment of the RNA 3'-end with substrate to form a catalysis-competent configuration. For the post-catalysis EC relaxation phase, we captured the long-sought, short-lived post-catalysis product state and identified a series of intermediates that reveal a reverse conformational transition that facilitates rapid translocation. Together, our findings define a comprehensive structural and dynamic framework for RNAPII NAC, yielding a "molecular movie" of RNAPII in action and revealing a fundamental principle by which the enzyme balances speed and fidelity through coordinated conformational dynamics.
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_54680.png

Downloads & links

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Map

FileDownload / File: emd_54680.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class D (frame8)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 348.192 Å		1.09 Å/pix.
x 320 pix.
= 348.192 Å		1.09 Å/pix.
x 320 pix.
= 348.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0881 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.4991461 - 0.9788932
Average (Standard dev.)0.0000064409105 (±0.02991862)
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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Half map: Half map A of CryoEM map of Yeast...

Fileemd_54680_half_map_1.map
AnnotationHalf map A of CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class D (frame8)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of CryoEM map of Yeast...

Fileemd_54680_half_map_2.map
AnnotationHalf map B of CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class D (frame8)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: UCSF Chimera, UCSF ChimeraX, PHENIX) / Number images used: 93475
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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