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- EMDB-61298: The structure of SMARCAD1 bound to the nucleosome in Apo state. -

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Basic information

Entry
Database: EMDB / ID: EMD-61298
TitleThe structure of SMARCAD1 bound to the nucleosome in Apo state.
Map data
Sample
  • Complex: The structure of SMARCAD1 bound to the nucleosome in Apo state.
KeywordsDNA / ligand / protein / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen ZC / Hu PJ / Sia YY / Chen KJ / Xia X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2025
Title: Subnucleosome preference of human chromatin remodeller SMARCAD1.
Authors: Pengjing Hu / Jingxi Sun / Hongyao Sun / Kangjing Chen / Youyang Sia / Xian Xia / Qiaoran Xi / Zhucheng Chen /
Abstract: Chromatin remodellers are pivotal in the regulation of nucleosome dynamics in cells, and they are important for chromatin packaging, transcription, replication and DNA repair. Here we show that the ...Chromatin remodellers are pivotal in the regulation of nucleosome dynamics in cells, and they are important for chromatin packaging, transcription, replication and DNA repair. Here we show that the human chromatin remodeller SMARCAD1 exhibits a substrate preference for subnucleosomal particles over the canonical nucleosome. Cryo-electron microscopy structures of SMARCAD1 bound to the nucleosome and hexasome provide mechanistic insights into the substrate selectivity. SMARCAD1 binds to the hexasome through multiple family-specific elements that are essential for the functions in vitro and in cells. The enzyme binds to the canonical nucleosome in an inactive conformation, which accounts for its diminished activity towards the nucleosome. Notably, the histone chaperone FACT complex acts synergistically with H2A-H2B to promote the activity of SMARCAD1 in nucleosome remodelling. Together, our findings reveal an avenue for chromatin regulation, whereby subnucleosomes are remodelled through an ATP-dependent process.
History
DepositionAug 25, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61298.png

Downloads & links

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Map

FileDownload / File: emd_61298.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 346.4 Å		1.08 Å/pix.
x 320 pix.
= 346.4 Å		1.08 Å/pix.
x 320 pix.
= 346.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0924
Minimum - Maximum-2.5623171 - 4.561993
Average (Standard dev.)0.002930225 (±0.051116288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61298_msk_1.map
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Half map: #2

Fileemd_61298_half_map_1.map
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Half map: #1

Fileemd_61298_half_map_2.map
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Sample components

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Entire : The structure of SMARCAD1 bound to the nucleosome in Apo state.

EntireName: The structure of SMARCAD1 bound to the nucleosome in Apo state.
Components
  • Complex: The structure of SMARCAD1 bound to the nucleosome in Apo state.

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Supramolecule #1: The structure of SMARCAD1 bound to the nucleosome in Apo state.

SupramoleculeName: The structure of SMARCAD1 bound to the nucleosome in Apo state.
type: complex / ID: 1 / Parent: 0
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: 7.5
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103023
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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