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- EMDB-22904: Low resolution map of the nucleosome deacetylase complex from mur... -

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Basic information

Entry
Database: EMDB / ID: EMD-22904
TitleLow resolution map of the nucleosome deacetylase complex from murine erythroleukemia cells.
Map dataMap of NuDe obtained from negative-stained electron microscopy, using the software package CryoSPARC.
Sample
  • Complex: The nucleosome deacetylase complex
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 20.0 Å
AuthorsJackman MJ / Landsberg MJ / Mackay JP
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1126357 Australia
CitationJournal: Cell Rep / Year: 2020
Title: The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture.
Authors: Jason K K Low / Ana P G Silva / Mehdi Sharifi Tabar / Mario Torrado / Sarah R Webb / Benjamin L Parker / Maryam Sana / Callum Smits / Jason W Schmidberger / Lou Brillault / Matthew J Jackman ...Authors: Jason K K Low / Ana P G Silva / Mehdi Sharifi Tabar / Mario Torrado / Sarah R Webb / Benjamin L Parker / Maryam Sana / Callum Smits / Jason W Schmidberger / Lou Brillault / Matthew J Jackman / David C Williams / Gerd A Blobel / Sandra B Hake / Nicholas E Shepherd / Michael J Landsberg / Joel P Mackay /
Abstract: The nucleosome remodeling and deacetylase (NuRD) complex is essential for metazoan development but has been refractory to biochemical analysis. We present an integrated analysis of the native ...The nucleosome remodeling and deacetylase (NuRD) complex is essential for metazoan development but has been refractory to biochemical analysis. We present an integrated analysis of the native mammalian NuRD complex, combining quantitative mass spectrometry, cross-linking, protein biochemistry, and electron microscopy to define the architecture of the complex. NuRD is built from a 2:2:4 (MTA, HDAC, and RBBP) deacetylase module and a 1:1:1 (MBD, GATAD2, and Chromodomain-Helicase-DNA-binding [CHD]) remodeling module, and the complex displays considerable structural dynamics. The enigmatic GATAD2 controls the asymmetry of the complex and directly recruits the CHD remodeler. The MTA-MBD interaction acts as a point of functional switching, with the transcriptional regulator PWWP2A competing with MBD for binding to the MTA-HDAC-RBBP subcomplex. Overall, our data address the long-running controversy over NuRD stoichiometry, provide imaging of the mammalian NuRD complex, and establish the biochemical mechanism by which PWWP2A can regulate NuRD composition.
History
DepositionOct 27, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.294
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.294
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22904.png

Downloads & links

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Map

FileDownload / File: emd_22904.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of NuDe obtained from negative-stained electron microscopy, using the software package CryoSPARC.
Voxel sizeX=Y=Z: 2.4 Å
Density
Contour LevelBy AUTHOR: 0.294 / Movie #1: 0.294
Minimum - Maximum-1.0947253 - 3.1702197
Average (Standard dev.)-0.023727752 (±0.1383911)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 614.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z614.400614.400614.400
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.0953.170-0.024

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Supplemental data

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Sample components

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Entire : The nucleosome deacetylase complex

EntireName: The nucleosome deacetylase complex
Components
  • Complex: The nucleosome deacetylase complex

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Supramolecule #1: The nucleosome deacetylase complex

SupramoleculeName: The nucleosome deacetylase complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Organ: Spleen / Location in cell: nucleus

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.2
StainingType: NEGATIVE / Material: uranyl acetate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: OTHER / Average electron dose: 100.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14019

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