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- EMDB-68371: Co-transcriptional histone H3K36 methylation complex containing R... -

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Entry
Database: EMDB / ID: EMD-68371
TitleCo-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, Spt6 reconstruction)
Map data
Sample
  • Complex: Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115)
Keywordschromatin / nucleosome / TRANSCRIPTION
Biological speciesKomagataella phaffii GS115 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsKujirai T / Ehara H / Ito T / Henmi M / Sekine S / Kurumizaka H
Funding support Japan, 12 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP24ama121009 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
Japan Society for the Promotion of Science (JSPS)JP24H00062 Japan
Japan Society for the Promotion of Science (JSPS)JP20H03201 Japan
Japan Society for the Promotion of Science (JSPS)JP23K17392 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15033 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05906 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Science and TechnologyJPMJCR24T3 Japan
Other privateDaiichi Sankyo Foundation for Life Science
CitationJournal: Sci Adv / Year: 2026
Title: Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT.
Authors: Tomoya Kujirai / Haruhiko Ehara / Tomoko Ito / Masami Henmi / Eriko Oya / Takehiko Kobayashi / Shun-Ichi Sekine / Hitoshi Kurumizaka /
Abstract: Trimethylation of the histone H3K36 residue (H3K36me3) plays an indispensable role in ensuring transcription fidelity by suppressing undesired cryptic transcription in chromatin. H3K36me3 ...Trimethylation of the histone H3K36 residue (H3K36me3) plays an indispensable role in ensuring transcription fidelity by suppressing undesired cryptic transcription in chromatin. H3K36me3 modification is accomplished by Set2/SETD2 during transcription elongation by the RNA polymerase II elongation complex (EC). Here, we found that Set2-mediated H3K36me3 deposition occurs on the nucleosome reassembling behind the EC. The histone chaperone FACT suppresses H3K36me3 deposition on the downstream nucleosome, thereby ensuring that Set2 targets specifically on the reassembling upstream nucleosome. Cryo-electron microscopy structures of the nucleosome-transcribing EC complexed with Set2 revealed that Set2 is anchored by the Spt6 subunit of the EC to capture both of the H3 N-terminal tails in a stepwise manner during the nucleosome reassembly process. Abrogation of the Set2-EC interaction leads to defective transcription-coupled H3K36me3 deposition. These insights elucidate the structure-based mechanism of transcription-coupled H3K36me3 deposition in chromatin.
History
DepositionJan 14, 2026-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68371.png

Downloads & links

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Map

FileDownload / File: emd_68371.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 220 pix.
= 324.5 Å		1.48 Å/pix.
x 220 pix.
= 324.5 Å		1.48 Å/pix.
x 220 pix.
= 324.5 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.475 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.037
Minimum - Maximum-0.05732514 - 0.15329899
Average (Standard dev.)0.00012978287 (±0.0028776957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 324.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68371_half_map_1.map
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Half map: #2

Fileemd_68371_half_map_2.map
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Sample components

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Entire : Co-transcriptional histone H3K36 methylation complex containing R...

EntireName: Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115)
Components
  • Complex: Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115)

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Supramolecule #1: Co-transcriptional histone H3K36 methylation complex containing R...

SupramoleculeName: Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Komagataella phaffii GS115 (fungus)

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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: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 183297
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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