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- EMDB-6700: Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the... -

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Basic information

Entry
Database: EMDB / ID: 6700
TitleComplex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome
SampleSHL2 complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataDensity map of Snf2-nucleosome complex with Snf2 binding to SHL2 of the nucleosome. The map was sharpened by RELION post-processing, and the resolution was reported at 4.69A.
Methodsingle particle reconstruction, at 4.69 Å resolution
AuthorsLi M / Liu X / Xia X / Cheng Z / Li X
CitationNature, 2017, 544, 440-445

Nature, 2017, 544, 440-445 StrPapers
Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure.
Xiaoyu Liu / Meijing Li / Xian Xia / Xueming Li / Zhucheng Chen

Validation ReportPDB-ID: 5x0y

SummaryFull reportAbout validation report
DateDeposition: Jan 23, 2017 / Header (metadata) release: Apr 19, 2017 / Map release: Apr 19, 2017 / Last update: Jun 7, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0341
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0341
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5x0y
  • Surface level: 0.0341
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_6700.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.0341 (by author), 0.0341 (movie #1):
Minimum - Maximum-0.038502302 - 0.092987455
Average (Standard dev.)0.00025256493 (0.002908369)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0390.0930.000

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Supplemental data

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Sample components

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Entire SHL2 complex

EntireName: SHL2 complex / Number of components: 8

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Component #1: protein, SHL2 complex

ProteinName: SHL2 complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Histone H3.2

ProteinName: Histone H3.2 / Recombinant expression: No
MassTheoretical: 15.289904 kDa
Source (engineered)Expression System: Xenopus laevis / amphibia / African clawed frog /

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Component #3: protein, Histone H4

ProteinName: Histone H4 / Recombinant expression: No
MassTheoretical: 11.263231 kDa
Source (engineered)Expression System: Xenopus laevis / amphibia / African clawed frog /

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Component #4: protein, Histone H2A

ProteinName: Histone H2A / Recombinant expression: No
MassTheoretical: 13.978241 kDa
Source (engineered)Expression System: Xenopus laevis / amphibia / African clawed frog /

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Component #5: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Recombinant expression: No
MassTheoretical: 13.524752 kDa
Source (engineered)Expression System: Xenopus laevis / amphibia / African clawed frog /

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Component #6: nucleic-acid, DNA (167-MER)

Nucleic-acidName: DNA (167-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT)(DA)(DG)(DC) (DT)(DT)(DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DG)(DT)(DA)(DC)(DG)(DA)(DT)
MassTheoretical: 51.381758 kDa

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Component #7: nucleic-acid, DNA (167-MER)

Nucleic-acidName: DNA (167-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DG)(DA)(DT)
MassTheoretical: 51.723949 kDa

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Component #8: protein, Transcription regulatory protein SNF2

ProteinName: Transcription regulatory protein SNF2 / Recombinant expression: No
MassTheoretical: 85.802805 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 90725
3D reconstructionSoftware: Relion / Resolution: 4.69 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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