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- EMDB-1877: CryoEM structure of the chromatin remodelling factor ISW1a bound ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1877
TitleCryoEM structure of the chromatin remodelling factor ISW1a bound to a mononucleosome (45N29)
Map dataSurface rendering of 45N29-ISW1a (delta ATPase)
Sample
  • Sample: Chromatin remodelling factor ISW1a (delta ATPase) bound to a mononucleosome (with 45 and 29 bp extensions).
  • Protein or peptide: Nucleosome
  • Protein or peptide: ISW1a
KeywordsNucleosome / chromatin remodelling factor / ISW1a / ISWI
Biological speciesXenopus laevis (African clawed frog) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsFrouws TD / Richmond TJ
CitationJournal: Nature / Year: 2011
Title: Structure and mechanism of the chromatin remodelling factor ISW1a.
Authors: Kazuhiro Yamada / Timothy D Frouws / Brigitte Angst / Daniel J Fitzgerald / Carl DeLuca / Kyoko Schimmele / David F Sargent / Timothy J Richmond /
Abstract: Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors ...Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors are implicated in establishing the nucleosome repeat during replication and altering nucleosome position to affect gene activity. Here we have solved the crystal structures of S. cerevisiae ISW1a lacking its ATPase domain both alone and with DNA bound at resolutions of 3.25 Å and 3.60 Å, respectively, and we have visualized two different nucleosome-containing remodelling complexes using cryo-electron microscopy. The composite X-ray and electron microscopy structures combined with site-directed photocrosslinking analyses of these complexes suggest that ISW1a uses a dinucleosome substrate for chromatin remodelling. Results from a remodelling assay corroborate the dinucleosome model. We show how a chromatin remodelling factor could set the spacing between two adjacent nucleosomes acting as a 'protein ruler'.
History
DepositionFeb 16, 2011-
Header (metadata) releaseFeb 18, 2011-
Map releaseApr 21, 2011-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1877imag...

Downloads & links

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Map

FileDownload / File: emd_1877.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendering of 45N29-ISW1a (delta ATPase)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 128 pix.
= 345.6 Å		2.7 Å/pix.
x 128 pix.
= 345.6 Å		2.7 Å/pix.
x 128 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.0718889 - 0.170402
Average (Standard dev.)0.000116232 (±0.0137858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 345.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z128128128
origin x/y/z-0.000-0.000-0.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0720.1700.000

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Supplemental data

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Sample components

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Entire : Chromatin remodelling factor ISW1a (delta ATPase) bound to a mono...

EntireName: Chromatin remodelling factor ISW1a (delta ATPase) bound to a mononucleosome (with 45 and 29 bp extensions).
Components
  • Sample: Chromatin remodelling factor ISW1a (delta ATPase) bound to a mononucleosome (with 45 and 29 bp extensions).
  • Protein or peptide: Nucleosome
  • Protein or peptide: ISW1a

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Supramolecule #1000: Chromatin remodelling factor ISW1a (delta ATPase) bound to a mono...

SupramoleculeName: Chromatin remodelling factor ISW1a (delta ATPase) bound to a mononucleosome (with 45 and 29 bp extensions).
type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 2
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: Nucleosome

MacromoleculeName: Nucleosome / type: protein_or_peptide / ID: 1 / Name.synonym: Nucleosome
Details: Nucleosomes consist of recombinant xenopus histones H2A,H2B,H3,H4, reconstituted onto '601' DNA with 45 and 29 bp extensions.
Recombinant expression: Yes
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 256 MDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #2: ISW1a

MacromoleculeName: ISW1a / type: protein_or_peptide / ID: 2 / Name.synonym: Remodelling factor
Details: Recombinant yeast ISW1a (delta ATPase) expressed with MultiBac system
Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 120 MDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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

Concentration3.5 mg/mL
BufferpH: 7.5 / Details: 10mM TrisCl, 10mM KCl, 0.1mM EDTA
GridDetails: C-flat 224
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK II / Details: Vitrification instrument: Vitribot MKII / Method: 0 offset, 4 sec blot, 1 sec drain

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 100 K
Specialist opticsEnergy filter - Name: Gatan
DetailsLow dose
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51606 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 80000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsSemi-automated picking in EMAN BOXER
CTF correctionDetails: Class averages
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: Start model created by common-lines, then iterated with projection matching.
Number images used: 13206
Final angle assignmentDetails: theta 90, phi 180
Final two d classificationNumber classes: 195

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Atomic model buiding 1

Initial modelPDB ID:

1kx5

SoftwareName: Chimera
DetailsManually fitted in Chimera, and missing DNA segments were built in.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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