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- EMDB-22895: Low resolution map of the nucleosome remodelling and deacetylase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-22895
TitleLow resolution map of the nucleosome remodelling and deacetylase complex from MEL cells.
Map dataMap of the nucleosome remodelling and deacetylase complex (NuRD) produced using negative-stained electron microscopy images analyzed in Cryosparc.
Sample
  • Complex: Endogenous nucleosome remodelling and deacetylase complex purified from MEL cells
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 14.0 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 26, 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: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22895.png

Downloads & links

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Map

FileDownload / File: emd_22895.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the nucleosome remodelling and deacetylase complex (NuRD) produced using negative-stained electron microscopy images analyzed in Cryosparc.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.17 Å/pix.
x 300 pix.
= 651. Å		2.17 Å/pix.
x 300 pix.
= 651. Å		2.17 Å/pix.
x 300 pix.
= 651. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.655235 - 4.7355237
Average (Standard dev.)-0.009246632 (±0.17418209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 651.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.172.172.17
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z651.000651.000651.000
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.6554.736-0.009

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Supplemental data

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Sample components

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Entire : Endogenous nucleosome remodelling and deacetylase complex purifie...

EntireName: Endogenous nucleosome remodelling and deacetylase complex purified from MEL cells
Components
  • Complex: Endogenous nucleosome remodelling and deacetylase complex purified from MEL cells

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Supramolecule #1: Endogenous nucleosome remodelling and deacetylase complex purifie...

SupramoleculeName: Endogenous nucleosome remodelling and deacetylase complex purified from MEL cells
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Purified using a GST-tagged column bound by a recombinant GST-FOG1 protein; crosslinked using GraFix
Source (natural)Organism: Mus musculus (house mouse) / Organ: Spleen / Organelle: Nucleus
Molecular weightExperimental: 955 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.2
StainingType: NEGATIVE / Material: Uranyl acetate

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 100.0 e/Å2
Details: Images recorded on a DE LC1100 lens coupled CCD detector. Estimated dose.
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2.14.2)
Startup modelType of model: NONE / Details: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111503
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.14.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final 3D classificationNumber classes: 3 / Avg.num./class: 42000 / Software - Name: cryoSPARC (ver. 2.14.2)

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