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- EMDB-53064: CryoEM structure of transcribing RNA polymerase II elongation com... -

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Basic information

Entry
Database: EMDB / ID: EMD-53064
TitleCryoEM structure of transcribing RNA polymerase II elongation complex_3D classification map containing the complete nucleic acid scaffold
Map dataCryoEM structure of transcribing RNA polymerase II elongation complex_3D classification map containing the complete nucleic acid scaffold.
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: Mol Cell / Year: 2026
Title: Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis.
Authors: Qingrong Li / Gangshun Yi / Yue Wu / Sophy Xu / Jenny Chong / Xuhui Huang / Peijun Zhang / Dong Wang /
Abstract: RNA polymerase II (RNA Pol II) is central to gene expression, but its catalytic mechanism remains elusive due to the absence of high-resolution structural data. The role of water molecules in RNA Pol ...RNA polymerase II (RNA Pol II) is central to gene expression, but its catalytic mechanism remains elusive due to the absence of high-resolution structural data. The role of water molecules in RNA Pol II catalysis is unknown. Here, we present 3 high-resolution cryo-electron microscopy structures of active Saccharomyces cerevisiae RNA Pol II elongation complexes in distinct catalytic states: two pre-catalysis states at 1.96 Å and 2.26 Å resolution and a post-catalysis state at 2.33 Å resolution. Each structure contains over 700-1,350 ordered water molecules, many located at functionally critical positions. Comparative analysis shows that these waters play essential roles in proton-transfer steps during RNA Pol II catalysis, facilitating substrate recognition and trigger-loop folding during nucleotide addition. Strikingly, these waters are conserved between prokaryotic and eukaryotic transcription machineries (see Mueller and Darst). These findings provide unprecedented mechanistic insights into RNA Pol II catalysis and reveal vital and evolutionarily conserved roles of water molecules in transcription.
History
DepositionMar 9, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53064.png

Downloads & links

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Map

FileDownload / File: emd_53064.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_3D classification map containing the complete nucleic acid scaffold.
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: 0.07
Minimum - Maximum-0.19806533 - 0.4467938
Average (Standard dev.)0.000012676724 (±0.016679822)
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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Half map: CryoEM structure of transcribing RNA polymerase II elongation...

Fileemd_53064_half_map_1.map
AnnotationCryoEM structure of transcribing RNA polymerase II elongation complex_half A map of 3D classification map containing the complete nucleic acid scaffold.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM structure of transcribing RNA polymerase II elongation...

Fileemd_53064_half_map_2.map
AnnotationCryoEM structure of transcribing RNA polymerase II elongation complex_half B map of 3D classification map containing the complete nucleic acid scaffold.
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: 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

Concentration1 mg/mL
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 / Instrument: FEI VITROBOT MARK II

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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: 50808
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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