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- EMDB-3502: Structural reorganization of the chromatin remodeling enzyme Chd1... -

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Basic information

Entry
Database: EMDB / ID: 3502
TitleStructural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
SampleChd1-Nucleosome complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Xenopus laevis / amphibia / African clawed frog /
Map dataStructure of S.cerevisiae chromatin remodeling enzyme Chd1 bound to Nucleosome.
Methodsingle particle reconstruction, at 15 Å resolution
AuthorsSundaramoorthy R / Owen-Hughes T
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.
Ramasubramanian Sundaramoorthy / Amanda L Hughes / Vijender Singh / Nicola Wiechens / Daniel P Ryan / Hassane El-Mkami / Maxim Petoukhov / Dmitri I Svergun / Barbara Treutlein / Salina Quack / Monika Fischer / Jens Michaelis / Bettina Böttcher / David G Norman / Tom Owen-Hughes

DateDeposition: Nov 15, 2016 / Header (metadata) release: Dec 14, 2016 / Map release: Apr 5, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.049
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.049
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_3502.map.gz (map file in CCP4 format, 62501 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
1.34 Å/pix.
= 335. Å
250 pix
1.34 Å/pix.
= 335. Å
250 pix
1.34 Å/pix.
= 335. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.049 (by author), 0.049 (movie #1):
Minimum - Maximum-0.054358844 - 0.20822248
Average (Standard dev.)0.0010571269 (0.012176228)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin000
Limit249249249
Spacing250250250
CellA=B=C: 335 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z335.000335.000335.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0540.2080.001

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Supplemental data

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Sample components

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Entire Chd1-Nucleosome complex

EntireName: Chd1-Nucleosome complex
Details: S.cerevisiae chromatin remodelling enzyme in complex with Nucleosome
Number of components: 3
MassTheoretical: 400 kDa

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Component #1: protein, Chd1-Nucleosome complex

ProteinName: Chd1-Nucleosome complex
Details: S.cerevisiae chromatin remodelling enzyme in complex with Nucleosome
Recombinant expression: No
MassTheoretical: 400 kDa

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Component #2: protein, chd1

ProteinName: chd1 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: protein, nucleosome

ProteinName: nucleosome / Recombinant expression: No
SourceSpecies: Xenopus laevis / amphibia / African clawed frog /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.2 mg/ml / Buffer solution: Solutions were made fresh / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.27 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 59000 X (nominal), 59000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800 - 4000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2560 / Sampling size: 14 microns
Details: Images are collected in movie mode at 22 images per second

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 52208
Details: The selected images were high pass filtered and framwise movie corrected for drift.
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 15 Å / Resolution method: FSC 0.143 CUT-OFF / Details: RELION 1.4 was used for the reconstruction.
FSC plot (resolution assessment)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Cross-correlation coefficient / Refinement space: REAL
Input PDB model: 1KX5, 3MWY, 3TED
Chain ID: A,B,C,D,E,F,G,H,I,J, 3MWY_A, A,B,C

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