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- EMDB-11712: HDAC-DC-nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-11712
TitleHDAC-DC-nucleosome
Map dataHDAC-DC-nucleosome
Sample
  • Complex: HDAC-PC-Nuc
    • Complex: Histone deacetylase
    • Complex: Histone
    • Complex: DNA
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / unidentified plasmid (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.6 Å
AuthorsLee J-H / Bollschweiler D / Schaefer T / Huber R
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Sci Adv / Year: 2021
Title: Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies.
Authors: Jung-Hoon Lee / Daniel Bollschweiler / Tillman Schäfer / Robert Huber /
Abstract: The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup ...The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo-electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda1-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification.
History
DepositionSep 9, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateFeb 17, 2021-
Current statusFeb 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11712.png

Downloads & links

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Map

FileDownload / File: emd_11712.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHDAC-DC-nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 256 pix.
= 482.56 Å		1.89 Å/pix.
x 256 pix.
= 482.56 Å		1.89 Å/pix.
x 256 pix.
= 482.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.20573889 - 1.1538204
Average (Standard dev.)0.000733406 (±0.035002667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 482.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8851.8851.885
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z482.560482.560482.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2061.1540.001

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Supplemental data

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Sample components

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Entire : HDAC-PC-Nuc

EntireName: HDAC-PC-Nuc
Components
  • Complex: HDAC-PC-Nuc
    • Complex: Histone deacetylase
    • Complex: Histone
    • Complex: DNA

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Supramolecule #1: HDAC-PC-Nuc

SupramoleculeName: HDAC-PC-Nuc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14

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Supramolecule #2: Histone deacetylase

SupramoleculeName: Histone deacetylase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Histone

SupramoleculeName: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#12
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #13-#14
Source (natural)Organism: unidentified plasmid (others)
Recombinant expressionOrganism: synthetic construct (others)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1) / Number images used: 9534
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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Atomic model buiding 1

DetailsReal space refinement

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