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- EMDB-54201: Activated elongation complex with IWS1 and ELOF1 - MAP4 - focused... -

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Basic information

Entry
Database: EMDB / ID: EMD-54201
TitleActivated elongation complex with IWS1 and ELOF1 - MAP4 - focused classification of PAF1 LEO1
Map data
Sample
  • Complex: Activated Elongation Complex (ECstar) with IWS1 and ELOF1
KeywordsRNA Pol II / Elongation / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsWalshe JL / Cramer P
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2025
Title: IWS1 positions downstream DNA to globally stimulate Pol II elongation.
Authors: Aiturgan Zheenbekova / James L Walshe / Moritz Ochmann / Moritz Bäuerle / Ute Neef / Kerstin C Maier / Petra Rus / Yumeng Yan / Henning Urlaub / Patrick Cramer / Kristina Žumer /
Abstract: The protein IWS1 (Interacts with SPT6 1) is implicated in transcription-associated processes, but a direct role in RNA polymerase (Pol) II function is unknown. Here, we use multi-omics kinetic ...The protein IWS1 (Interacts with SPT6 1) is implicated in transcription-associated processes, but a direct role in RNA polymerase (Pol) II function is unknown. Here, we use multi-omics kinetic analysis after rapid depletion of IWS1 in human cells to show that loss of IWS1 results in a global decrease of RNA synthesis and a global reduction in Pol II elongation velocity. We then resolve the cryo-EM structure of the activated Pol II elongation complex with bound IWS1 and elongation factor ELOF1 and show that IWS1 acts as a scaffold and positions downstream DNA within the cleft of Pol II. In vitro assays show that the disordered C-terminal region of IWS1 that contacts the cleft of Pol II is responsible for stimulation of Pol II activity and is aided by ELOF1. Finally, we find that the defect in transcription upon IWS1 depletion leads to a decrease of histone H3 tri-methylation at residue lysine-36 (H3K36me3), but that this secondary effect is an indirect function of IWS1. In summary, our structure-function analysis establishes IWS1 as a Pol II-associated elongation factor that acts globally to stimulate Pol II elongation velocity and ensure proper co-transcriptional histone methylation.
History
DepositionJun 30, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54201.png

Downloads & links

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Map

FileDownload / File: emd_54201.map.gz / Format: CCP4 / Size: 30.5 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 200 pix.
= 210. Å		1.05 Å/pix.
x 200 pix.
= 210. Å		1.05 Å/pix.
x 200 pix.
= 210. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.43014643 - 1.079469
Average (Standard dev.)0.006961061 (±0.030770067)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 209.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54201_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_54201_half_map_2.map
Projections & Slices
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Sample components

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Entire : Activated Elongation Complex (ECstar) with IWS1 and ELOF1

EntireName: Activated Elongation Complex (ECstar) with IWS1 and ELOF1
Components
  • Complex: Activated Elongation Complex (ECstar) with IWS1 and ELOF1

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Supramolecule #1: Activated Elongation Complex (ECstar) with IWS1 and ELOF1

SupramoleculeName: Activated Elongation Complex (ECstar) with IWS1 and ELOF1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1315755.43 MDa

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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: 40.03 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: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 175394
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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