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- EMDB-51239: Nucleosome portion of SHN103, unsharpened focused refinement. -

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Basic information

Entry
Database: EMDB / ID: EMD-51239
TitleNucleosome portion of SHN103, unsharpened focused refinement.
Map dataNucleosome portion of SHN103, unsharpened focus refinement.
Sample
  • Complex: Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Keywordschromatin / remodeling / transcription / nucleosome / DNA BINDING PROTEIN
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsEngeholm M / Roske JJ / Oberbeckmann E / Dienemann C / Lidschreiber M / Cramer P / Farnung L
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC)European Union
CitationJournal: Mol Cell / Year: 2024
Title: Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT.
Authors: Maik Engeholm / Johann J Roske / Elisa Oberbeckmann / Christian Dienemann / Michael Lidschreiber / Patrick Cramer / Lucas Farnung /
Abstract: To maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase ...To maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase II (RNAPII) generates hexasomes that occur directly adjacent to nucleosomes. The resulting hexasome-nucleosome complexes are then resolved by Chd1. We present two cryoelectron microscopy (cryo-EM) structures of Chd1 bound to a hexasome-nucleosome complex before and after restoration of the missing inner H2A/H2B dimer by FACT. Chd1 uniquely interacts with the complex, positioning its ATPase domain to shift the hexasome away from the nucleosome. In the absence of the inner H2A/H2B dimer, its DNA-binding domain (DBD) packs against the ATPase domain, suggesting an inhibited state. Restoration of the dimer by FACT triggers a rearrangement that displaces the DBD and stimulates Chd1 remodeling. Our results demonstrate how chromatin remodelers interact with a complex nucleosome assembly and suggest how Chd1 and FACT jointly support transcription by RNAPII.
History
DepositionAug 4, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51239.png

Downloads & links

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Map

FileDownload / File: emd_51239.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNucleosome portion of SHN103, unsharpened focus refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 320 pix.
= 393.6 Å		1.23 Å/pix.
x 320 pix.
= 393.6 Å		1.23 Å/pix.
x 320 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.59961724 - 1.9829355
Average (Standard dev.)-0.0021827864 (±0.031170841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51239_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_51239_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51239_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.

EntireName: Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Components
  • Complex: Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.

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Supramolecule #1: Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.

SupramoleculeName: Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.1 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143477
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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