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- EMDB-54538: State 1 MAP1 RNA Pol II activated elongation complex with SETD2 a... -

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Basic information

Entry
Database: EMDB / ID: EMD-54538
TitleState 1 MAP1 RNA Pol II activated elongation complex with SETD2 and upstream hexasome
Map data
Sample
  • Complex: State 2 SETD2 bound to proximal H3 tail
KeywordsRNA Pol II Activated elongation complex Co-transcriptional H3K36me3 SETD2 / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 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_54538.png

Downloads & links

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Map

FileDownload / File: emd_54538.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 537.6 Å		1.05 Å/pix.
x 512 pix.
= 537.6 Å		1.05 Å/pix.
x 512 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.03200723 - 0.06745735
Average (Standard dev.)0.00007487388 (±0.00090919394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54538_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_54538_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : State 2 SETD2 bound to proximal H3 tail

EntireName: State 2 SETD2 bound to proximal H3 tail
Components
  • Complex: State 2 SETD2 bound to proximal H3 tail

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Supramolecule #1: State 2 SETD2 bound to proximal H3 tail

SupramoleculeName: State 2 SETD2 bound to proximal H3 tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4-#5
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: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 231990
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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