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- EMDB-63139: Structure of motor2 of isw1-nucleosome double-bound complex in AD... -

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Basic information

Entry
Database: EMDB / ID: EMD-63139
TitleStructure of motor2 of isw1-nucleosome double-bound complex in ADP-ADP+ state
Map data
Sample
  • Complex: Structure of motor2 of isw1-nucleosome double-bound complex in ADP-ADP+ state
KeywordsChromatin Remodeler / Nucleosome / DNA BINDING PROTEIN
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSia Y / Pan H / Chen Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2025
Title: Structural insights into chromatin remodeling by ISWI during active ATP hydrolysis.
Authors: Youyang Sia / Han Pan / Kangjing Chen / Zhucheng Chen /
Abstract: Chromatin remodelers utilize the energy of adenosine triphosphate (ATP) hydrolysis to slide nucleosomes, regulating chromatin structure and gene activity in cells. In this work, we report structures ...Chromatin remodelers utilize the energy of adenosine triphosphate (ATP) hydrolysis to slide nucleosomes, regulating chromatin structure and gene activity in cells. In this work, we report structures of imitation switch (ISWI) bound to the nucleosome during active ATP hydrolysis and remodeling, revealing conformational transitions of the remodeling motor across the adenosine triphosphatase (ATPase) cycle. The DNA strands were distorted accordingly, showing one full base-pair bulge and a loss of histone contact at the site of motor binding in the adenosine diphosphate* (ADP*) and apo* (unbound) states. We also identified several important elements for regulation of the remodeling activity. Notably, an enzyme conformation exiting the remodeling cycle reveals a linker DNA-sensing brake mechanism. Together, our findings elucidate a multistate model of ISWI action, providing a comprehensive mechanism of DNA translocation and regulation underpinning chromatin remodeling.
History
DepositionJan 14, 2025-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63139.png

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Map

FileDownload / File: emd_63139.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.15861356 - 0.33169213
Average (Standard dev.)-0.00020589272 (±0.00443783)
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_63139_msk_1.map
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Half map: #1

Fileemd_63139_half_map_1.map
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Half map: #2

Fileemd_63139_half_map_2.map
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Sample components

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Entire : Structure of motor2 of isw1-nucleosome double-bound complex in AD...

EntireName: Structure of motor2 of isw1-nucleosome double-bound complex in ADP-ADP+ state
Components
  • Complex: Structure of motor2 of isw1-nucleosome double-bound complex in ADP-ADP+ state

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Supramolecule #1: Structure of motor2 of isw1-nucleosome double-bound complex in AD...

SupramoleculeName: Structure of motor2 of isw1-nucleosome double-bound complex in ADP-ADP+ state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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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: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154464
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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