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- EMDB-3517: Structural reorganization of the chromatin remodeling enzyme Chd1... -

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Basic information

Entry
Database: EMDB / ID: 3517
TitleStructural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.
Map dataS.Cerevisiae Chd1 bound to 601-Nucleosome
SampleChd1-Nucleosome complex
  • Chd1
  • Nucleosome
Function / homologyDomain of unknown function DUF4208 / SNF2 family N-terminal domain / Chromo domain / Chromo domain, conserved site / Chromo-like domain superfamily / Helicase superfamily 1/2, ATP-binding domain / Homeobox-like domain superfamily / Helicase, C-terminal / Chromo/chromo shadow domain / SNF2-related, N-terminal domain ...Domain of unknown function DUF4208 / SNF2 family N-terminal domain / Chromo domain / Chromo domain, conserved site / Chromo-like domain superfamily / Helicase superfamily 1/2, ATP-binding domain / Homeobox-like domain superfamily / Helicase, C-terminal / Chromo/chromo shadow domain / SNF2-related, N-terminal domain / P-loop containing nucleoside triphosphate hydrolase / SNF2-like, N-terminal domain superfamily / Chromo domain-containing protein 1 / Superfamilies 1 and 2 helicase C-terminal domain profile. / Helicase conserved C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Chromo and chromo shadow domain profile. / Chromo (CHRromatin Organisation MOdifier) domain / Chromo domain signature. / Domain of unknown function (DUF4208) / histone H2B conserved C-terminal lysine ubiquitination / negative regulation of histone exchange / nucleosome-dependent ATPase activity / nucleolar chromatin / negative regulation of DNA-dependent DNA replication / negative regulation of histone H3-K14 acetylation / regulation of chromatin organization / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of nucleosome density / SLIK (SAGA-like) complex / nucleosome mobilization / nucleosome organization / nucleosome positioning / SAGA complex / negative regulation of histone H3-K9 acetylation / rDNA binding / termination of RNA polymerase I transcription / ATP-dependent chromatin remodeling / ec:3.6.4.-: / DNA-dependent ATPase activity / termination of RNA polymerase II transcription / transcription elongation from RNA polymerase II promoter / chromatin DNA binding / methylated histone binding / helicase activity / transcription regulatory region DNA binding / nuclear chromatin / DNA binding / ATP binding / Chromo domain-containing protein 1
Function and homology information
SourceSaccharomyces cerevisiae / Yeast / yeast /
Xenopus laevis / African clawed frog / amphibia / African clawed frog /
Methodsingle particle reconstruction / cryo EM / 20 Å resolution
AuthorsSundaramoorthy R / Owen-Hughes T
CitationJournal: Elife / Year: 2017
Title: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.
Authors: 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
Abstract: The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding ...The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.
DateDeposition: Nov 25, 2016 / Header (metadata) release: Dec 28, 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: 0.0145
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3517.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.58 Å/pix.
= 316. Å
200 pix
1.58 Å/pix.
= 316. Å
200 pix
1.58 Å/pix.
= 316. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density
Contour Level:0.0145 (by author), 0.0145 (movie #1):
Minimum - Maximum-0.021911494 - 0.14400715
Average (Standard dev.)0.0008408567 (0.0077083986)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 316 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.581.581.58
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z316.000316.000316.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0220.1440.001

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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 601-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 601-nucleosome
Recombinant expression: No
MassTheoretical: 400 kDa

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Component #2: protein, Chd1

ProteinName: Chd1 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / Yeast / yeast /
Source (engineered)Expression System: Escherichia coli / / bacteria /

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Component #3: protein, Nucleosome

ProteinName: Nucleosome / Recombinant expression: No
SourceSpecies: Xenopus laevis / African clawed frog / amphibia / African clawed frog /
Source (engineered)Expression System: Escherichia coli / / bacteria /

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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 %
Details: Grids are double side blotted with 2sec blotting time and blotting force 10

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Details: Preliminary grid screen was done manually and then data collection was performed automatically using EMTools-EMMenu
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 22 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 68000 X (nominal), 68000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 5000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 70 - 70 K)
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 140 / Sampling size: 15.6 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 36324
Details: Images were manually inspected for any contamination or damage.
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 20 Å / Resolution method: FSC 0.143 CUT-OFF
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, 2XB0
Chain ID: A,B,C,D,E,F,G,H,I,J, 3MWY_A, 2XB0_X

Overall bvalue: 2800

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