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- EMDB-44110: Cryo-EM structure of native SWR1 bound to DNA (unmasked refinemen... -

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Basic information

Entry
Database: EMDB / ID: EMD-44110
TitleCryo-EM structure of native SWR1 bound to DNA (unmasked refinement filtered by local resolution)
Map data
Sample
  • Complex: Native SWR1 bound to DNA.
    • Complex: Native SWR1 complex
KeywordsChromatin Remodeler / Snf2 family ATPase / histone exchange / H2A.Z / GENE REGULATION
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLouder RK / Park G / Wu C
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149291 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125831 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM133151 United States
CitationJournal: Cell / Year: 2024
Title: Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler.
Authors: Robert K Louder / Giho Park / Ziyang Ye / Justin S Cha / Anne M Gardner / Qin Lei / Anand Ranjan / Eva Höllmüller / Florian Stengel / B Franklin Pugh / Carl Wu /
Abstract: The SWR1 chromatin remodeling complex is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. ...The SWR1 chromatin remodeling complex is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here, we use cryoelectron microscopy (cryo-EM) to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1-promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure, enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 toward the +1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.
History
DepositionMar 15, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44110.png

Downloads & links

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Map

FileDownload / File: emd_44110.map.gz / Format: CCP4 / Size: 216 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.)
1.03 Å/pix.
x 384 pix.
= 395.52 Å		1.03 Å/pix.
x 384 pix.
= 395.52 Å		1.03 Å/pix.
x 384 pix.
= 395.52 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.23734474 - 0.37045538
Average (Standard dev.)0.0000024068624 (±0.005619239)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44110_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44110_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Native SWR1 bound to DNA.

EntireName: Native SWR1 bound to DNA.
Components
  • Complex: Native SWR1 bound to DNA.
    • Complex: Native SWR1 complex

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Supramolecule #1: Native SWR1 bound to DNA.

SupramoleculeName: Native SWR1 bound to DNA. / type: complex / ID: 1 / Parent: 0
Details: Endogenously purified yeast SWR1 complex bound to 147-bp dsDNA fragment in the presence of ATPgS.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303
Molecular weightTheoretical: 1.19 MDa

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Supramolecule #2: Native SWR1 complex

SupramoleculeName: Native SWR1 complex / type: complex / ID: 2 / Parent: 1 / Details: Endogenously purified yeast SWR1 complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

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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

Concentration0.125 mg/mL
BufferpH: 7.6
Component:
ConcentrationNameFormula
20.0 mMHEPES
0.2 mMEDTA
2.0 mMmagnesium chlorideMgCl2
100.0 mMsodium chlorideNaCl
0.01 %IGEPAL CA-630
0.25 mMTCEP
1.0 mMATP-gamma-S
0.05 %glutaraldehyde

Details: 20 mM HEPES pH 7.6, 0.2 mM EDTA, 2 mM MgCl2, 100 mM NaCl, 0.01% IGEPAL CA-630, 3.5% glycerol, and 0.25 mM TCEP, 1 mM ATP-gamma-s, 0.05% glutaraldehyde.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 6 second blot time and blot force of 12..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5379 / Average exposure time: 4.0 sec. / Average electron dose: 54.0 e/Å2
Details: Each micrograph was fractionated into 64 frames within a 4 second exposure.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 48543 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 386667
Details: 2D classification was used to remove graphene edges.
Startup modelType of model: EMDB MAP
EMDB ID:

4395

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 101246
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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