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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
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.
SampleSHL2 complex
Function/homologypositive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation / cellular alcohol catabolic process / positive regulation of invasive growth in response to glucose limitation / positive regulation of mating type switching / Snf2, ATP coupling domain / QLQ domain profile. / Glutamine-Leucine-Glutamine, QLQ / sucrose catabolic process / |QLQ ...positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation / cellular alcohol catabolic process / positive regulation of invasive growth in response to glucose limitation / positive regulation of mating type switching / Snf2, ATP coupling domain / QLQ domain profile. / Glutamine-Leucine-Glutamine, QLQ / sucrose catabolic process / |QLQ / Snf2-ATP coupling, chromatin remodelling complex / HSA domain profile. / Helicase/SANT-associated domain / |HSA / AT hook, DNA-binding motif / nucleosome mobilization / SWI/SNF complex / strand invasion / rDNA binding / SNF2-related, N-terminal domain / ATP-dependent chromatin remodeling / SNF2 family N-terminal domain / ec:3.6.4.-: / Histone H2B / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2A / Histone H2A, C-terminal domain / TATA box binding protein associated factor (TAF) / Histone H4 / Histone H4 signature. / Histone H4, conserved site / CENP-T/Histone H4, histone fold / DNA-dependent ATPase activity / RNA polymerase II activating transcription factor binding / C-terminus of histone H2A / nucleosomal DNA binding / DNA-templated transcription, initiation / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3/CENP-A / lysine-acetylated histone binding / double-strand break repair / Histone H2A/H2B/H3 / nucleosome / helicase activity / DNA-dependent DNA replication / Histone-fold / nucleosome assembly / Helicase conserved C-terminal domain / Core histone H2A/H2B/H3/H4 / chromatin remodeling / Superfamilies 1 and 2 helicase C-terminal domain profile. / Bromodomain, conserved site / Bromodomain signature. / Bromodomain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Bromodomain / Helicase, C-terminal / Bromodomain-like superfamily / Helicase superfamily 1/2, ATP-binding domain / |Bromodomain / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / P-loop containing nucleoside triphosphate hydrolase / transcription, DNA-templated / DNA binding / nucleoplasm / ATP binding / nucleus / Histone H2B 1.1 / Histone H2A type 1 / Transcription regulatory protein SNF2 / Histone H4 / Histone H3.2 / Histone H2A
Function and homology information
SourceSaccharomyces cerevisiae / yeast / /
Methodsingle particle reconstruction, at 4.69 Å resolution
AuthorsLi M / Liu X / Xia X / Cheng Z / Li X
CitationJournal: Nature / Year: 2017
Title: Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure.
Authors: Xiaoyu Liu / Meijing Li / Xian Xia / Xueming Li / Zhucheng Chen
Abstract: Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron ...Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling. Snf2 binds to the phosphate backbones of one DNA gyre of the nucleosome mainly through its helicase motifs within the major domain cleft, suggesting a conserved mechanism of substrate engagement across different remodellers. Snf2 contacts the second DNA gyre via a positively charged surface, providing a mechanism to anchor the remodeller at a fixed position of the nucleosome. Snf2 locally deforms nucleosomal DNA at the site of binding, priming the substrate for the remodelling reaction. Together, these findings provide mechanistic insights into chromatin remodelling.
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
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5x0y
  • Surface level: 0.0341
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
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 / / / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli / bacteria / /

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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 / 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 / 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 / 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 / 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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