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- EMDB-2385: Negative stain electron microscopy of yeast INO80 -

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Basic information

Entry
Database: EMDB / ID: EMD-2385
TitleNegative stain electron microscopy of yeast INO80
Map dataReconstruction of chromatin remodeler INO80
Sample
  • Sample: S. cerevisiae INO80 chromatin remodeler
  • Protein or peptide: INO80
Keywordschromatin remodeler
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / Resolution: 22.0 Å
AuthorsTosi A / Haas C / Herzog F / Gilmozzi A / Berninghausen O / Ungewickell C / Gerhold CB / Lakomek K / Aebersold R / Beckmann R / Hopfner KP
CitationJournal: Cell / Year: 2013
Title: Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex.
Authors: Alessandro Tosi / Caroline Haas / Franz Herzog / Andrea Gilmozzi / Otto Berninghausen / Charlotte Ungewickell / Christian B Gerhold / Kristina Lakomek / Ruedi Aebersold / Roland Beckmann / Karl-Peter Hopfner /
Abstract: INO80/SWR1 family chromatin remodelers are complexes composed of >15 subunits and molecular masses exceeding 1 MDa. Their important role in transcription and genome maintenance is exchanging the ...INO80/SWR1 family chromatin remodelers are complexes composed of >15 subunits and molecular masses exceeding 1 MDa. Their important role in transcription and genome maintenance is exchanging the histone variants H2A and H2A.Z. We report the architecture of S. cerevisiae INO80 using an integrative approach of electron microscopy, crosslinking and mass spectrometry. INO80 has an embryo-shaped head-neck-body-foot architecture and shows dynamic open and closed conformations. We can assign an Rvb1/Rvb2 heterododecamer to the head in close contact with the Ino80 Snf2 domain, Ies2, and the Arp5 module at the neck. The high-affinity nucleosome-binding Nhp10 module localizes to the body, whereas the module that contains actin, Arp4, and Arp8 maps to the foot. Structural and biochemical analyses indicate that the nucleosome is bound at the concave surface near the neck, flanked by the Rvb1/2 and Arp8 modules. Our analysis establishes a structural and functional framework for this family of large remodelers.
History
DepositionMay 27, 2013-
Header (metadata) releaseJun 19, 2013-
Map releaseOct 2, 2013-
UpdateOct 2, 2013-
Current statusOct 2, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2385.tif

Downloads & links

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Map

FileDownload / File: emd_2385.map.gz / Format: CCP4 / Size: 20.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of chromatin remodeler INO80
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.31 Å/pix.
x 176 pix.
= 582.56 Å		3.31 Å/pix.
x 176 pix.
= 582.56 Å		3.31 Å/pix.
x 176 pix.
= 582.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.003 / Movie #1: 0.012
Minimum - Maximum-0.05804853 - 0.10568224
Average (Standard dev.)-0.00024482 (±0.00300771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 582.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.313.313.31
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z582.560582.560582.560
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS176176176
D min/max/mean-0.0580.106-0.000

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Supplemental data

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Sample components

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Entire : S. cerevisiae INO80 chromatin remodeler

EntireName: S. cerevisiae INO80 chromatin remodeler
Components
  • Sample: S. cerevisiae INO80 chromatin remodeler
  • Protein or peptide: INO80

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Supramolecule #1000: S. cerevisiae INO80 chromatin remodeler

SupramoleculeName: S. cerevisiae INO80 chromatin remodeler / type: sample / ID: 1000 / Details: The sample was monodisperse (size exclusion) / Oligomeric state: Dodecameric Rvb1/2 / Number unique components: 15
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: INO80

MacromoleculeName: INO80 / type: protein_or_peptide / ID: 1 / Oligomeric state: Dodecamer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: baker's yeast
Molecular weightTheoretical: 1.3 MDa

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeOTHER
DateAug 31, 2011
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, EMAN2, Sparx / Number images used: 14386

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