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- EMDB-5638: 3D Cryo-negative EM structure of nucleosome-bound SWR1 -

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Basic information

Entry
Database: EMDB / ID: EMD-5638
Title3D Cryo-negative EM structure of nucleosome-bound SWR1
Map dataCryo-EM structure of SWR1 (S.c.) bound to recombinant nucleosomes
Sample
  • Sample: SWR1 (S.c.) bound to recombinant nucleosomes
  • Protein or peptide: SWR1
Keywordschromatin remodeling / SWR1 / INO80 / nucleosome / Rvb1 / Rvb2 / AAA+ ATPase / histone / dimer exchange / H2A.Z
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 34.0 Å
AuthorsNguyen VQ / Ranjan A / Stengel F / Wei D / Aebersold R / Wu C / Leschziner AE
CitationJournal: Cell / Year: 2013
Title: Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1.
Authors: Vu Q Nguyen / Anand Ranjan / Florian Stengel / Debbie Wei / Ruedi Aebersold / Carl Wu / Andres E Leschziner /
Abstract: The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This ...The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.
History
DepositionApr 8, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseSep 25, 2013-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5638.png

Downloads & links

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Map

FileDownload / File: emd_5638.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of SWR1 (S.c.) bound to recombinant nucleosomes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.45 Å/pix.
x 150 pix.
= 517.5 Å		3.45 Å/pix.
x 150 pix.
= 517.5 Å		3.45 Å/pix.
x 150 pix.
= 517.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.04571663 - 0.13555907
Average (Standard dev.)-0.00058935 (±0.00814855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 517.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.453.453.45
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z517.500517.500517.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0460.136-0.001

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Supplemental data

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Sample components

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Entire : SWR1 (S.c.) bound to recombinant nucleosomes

EntireName: SWR1 (S.c.) bound to recombinant nucleosomes
Components
  • Sample: SWR1 (S.c.) bound to recombinant nucleosomes
  • Protein or peptide: SWR1

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Supramolecule #1000: SWR1 (S.c.) bound to recombinant nucleosomes

SupramoleculeName: SWR1 (S.c.) bound to recombinant nucleosomes / type: sample / ID: 1000 / Number unique components: 15
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: SWR1

MacromoleculeName: SWR1 / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W1588C-4C / synonym: Baker's yeast
Molecular weightTheoretical: 1.2 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 25 mM HEPES-KOH, pH 7.6, 1 mM EDTA, 2 mM MgCl2, 0.01% NP-40, 1 mM DTT, 100 mM KCl
StainingType: NEGATIVE
Details: Cryo-negative staining with 2% uranyl formate followed by freezing in liquid nitrogen
GridDetails: 200 mesh Quantifoil with glow-discharged thin carbon support
VitrificationCryogen name: NITROGEN / Instrument: OTHER
Method: Cryo-negative stain with 2% uranyl formate. Blotted and frozen in liquid nitrogen.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 100 K
DetailsLow-dose imaging
DateMay 20, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 300 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 86700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe dataset was classified using the maximum-likelihood based method in the RELION program. A selected 3D class was then refined against particles assigned to the class using RELION's "Autorefine" function.
CTF correctionDetails: EMAN2
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 12000

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