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- EMDB-54541: State 1 MAP2 RNA Pol II activated elongation complex with SETD2 a... -

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Basic information

Entry
Database: EMDB / ID: EMD-54541
TitleState 1 MAP2 RNA Pol II activated elongation complex with SETD2 and upstream hexasome
Map data
Sample
  • Complex: State 1 RNA Pol II activated elongation complex with SETD2 and upstream hexasome
KeywordsRNA Pol II Activated elongation complex Co-transcriptional H3K36me3 SETD2 / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsWalshe JL / Ochmann M / Dienemann C / Cramer P
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2025
Title: Molecular mechanism of co-transcriptional H3K36 methylation by SETD2.
Authors: James L Walshe / Moritz Ochmann / Ute Neef / Olexandr Dybkov / Christian Dienemann / Christiane Oberthür / Aiturgan Zheenbekova / Henning Urlaub / Patrick Cramer /
Abstract: H3K36me3 is a hallmark of actively and recently transcribed genes and contributes to cellular memory and identity. The deposition of H3K36me3 occurs co-transcriptionally when the methyltransferase ...H3K36me3 is a hallmark of actively and recently transcribed genes and contributes to cellular memory and identity. The deposition of H3K36me3 occurs co-transcriptionally when the methyltransferase SETD2 associates with RNA polymerase II. Here we present three cryo-EM structures of SETD2 bound to RNA polymerase II elongation complexes at different states of nucleosome passage. Together with functional probing, our results suggest a 3-step mechanism of transcription-coupled H3K36me3 deposition. First, binding to the elongation factor SPT6 tethers the catalytic SET domain in proximity to the upstream DNA. Second, RNA polymerase II nucleosome passage leads to the transfer of a hexasome from downstream to upstream, poised for methylation. Finally, continued transcription leads to upstream nucleosome reassembly, partial dissociation of the histone chaperone FACT and sequential methylation of both H3 tails, completing H3K36me3 deposition of an upstream nucleosome after RNA polymerase II passage.
History
DepositionJul 24, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54541.png

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Map

FileDownload / File: emd_54541.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 350 pix.
= 367.5 Å		1.05 Å/pix.
x 350 pix.
= 367.5 Å		1.05 Å/pix.
x 350 pix.
= 367.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.025749115 - 0.06320996
Average (Standard dev.)0.00012842595 (±0.0011344478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 367.49997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54541_half_map_1.map
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Half map: #2

Fileemd_54541_half_map_2.map
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Sample components

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Entire : State 1 RNA Pol II activated elongation complex with SETD2 and up...

EntireName: State 1 RNA Pol II activated elongation complex with SETD2 and upstream hexasome
Components
  • Complex: State 1 RNA Pol II activated elongation complex with SETD2 and upstream hexasome

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Supramolecule #1: State 1 RNA Pol II activated elongation complex with SETD2 and up...

SupramoleculeName: State 1 RNA Pol II activated elongation complex with SETD2 and upstream hexasome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30, #32, #31
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.83 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 112302
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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