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- EMDB-3607: SWR1 chromatin remodelling complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3607
TitleSWR1 chromatin remodelling complex
Map dataSWR1 chromatin remodelling complex
Sample
  • Complex: SWR1 chromatin remodelling complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsChaban Y / Lin C-L / Wigley DB
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Functional characterization and architecture of recombinant yeast SWR1 histone exchange complex.
Authors: Chia-Liang Lin / Yuriy Chaban / David M Rees / Elizabeth A McCormack / Lorraine Ocloo / Dale B Wigley /
Abstract: We have prepared recombinant fourteen subunit yeast SWR1 complex from insect cells using a modified MultiBac system. The 1.07 MDa recombinant protein complex has histone-exchange activity. Full ...We have prepared recombinant fourteen subunit yeast SWR1 complex from insect cells using a modified MultiBac system. The 1.07 MDa recombinant protein complex has histone-exchange activity. Full exchange activity is realized with a single SWR1 complex bound to a nucleosome. We also prepared mutant complexes that lack a variety of subunits or combinations of subunits and these start to reveal roles for some of these subunits as well as indicating interactions between them in the full complex. Complexes containing a series of N-terminally and C-terminally truncated Swr1 subunits reveal further details about interactions between subunits as well as their binding sites on the Swr1 subunit. Finally, we present electron microscopy studies revealing the dynamic nature of the complex and a 21 Å resolution reconstruction of the intact complex provides details not apparent in previously reported structures, including a large central cavity of sufficient size to accommodate a nucleosome.
History
DepositionFeb 28, 2017-
Header (metadata) releaseMar 15, 2017-
Map releaseMay 24, 2017-
UpdateSep 13, 2017-
Current statusSep 13, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3607.png

Downloads & links

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Map

FileDownload / File: emd_3607.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSWR1 chromatin remodelling complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.75 Å/pix.
x 128 pix.
= 352. Å		2.75 Å/pix.
x 128 pix.
= 352. Å		2.75 Å/pix.
x 128 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.091313325 - 0.32247585
Average (Standard dev.)0.002515694 (±0.017522343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.752.752.75
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.0910.3220.003

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Supplemental data

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Sample components

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Entire : SWR1 chromatin remodelling complex

EntireName: SWR1 chromatin remodelling complex
Components
  • Complex: SWR1 chromatin remodelling complex

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Supramolecule #1: SWR1 chromatin remodelling complex

SupramoleculeName: SWR1 chromatin remodelling complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Initial 3D model was obtained from 2D class averages using angular reconstitution technique.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 6000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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