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- EMDB-3399: Structure of the core NuRD complex (MTA1:HDAC1:RBBP4) -

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Basic information

Entry
Database: EMDB / ID: EMD-3399
TitleStructure of the core NuRD complex (MTA1:HDAC1:RBBP4)
Map dataStructure of the core NuRD complex: MTA1:HDAC1:RBBP4
Sample
  • Sample: Core NuRD complex (MTA1:HDAC1:RBBP4)
  • Ligand: MTA1
  • Ligand: HDAC1
  • Ligand: RBBP4
KeywordsTranscription / HDAC1 / MTA1 / RBBP4 / Chromatin / Histone Deacetylase / Metastasis associated protein / Histone binding protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
AuthorsMillard CJ / Saleh A / Morris K / Fairall L / Smith CJ / Schwabe JWR
CitationJournal: Elife / Year: 2016
Title: The structure of the core NuRD repression complex provides insights into its interaction with chromatin.
Authors: Christopher J Millard / Niranjan Varma / Almutasem Saleh / Kyle Morris / Peter J Watson / Andrew R Bottrill / Louise Fairall / Corinne J Smith / John W R Schwabe /
Abstract: The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure ...The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin.
History
DepositionMar 24, 2016-
Header (metadata) releaseApr 13, 2016-
Map releaseMay 18, 2016-
UpdateMay 18, 2016-
Current statusMay 18, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3399.tif

Downloads & links

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Map

FileDownload / File: emd_3399.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the core NuRD complex: MTA1:HDAC1:RBBP4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.92 Å/pix.
x 224 pix.
= 430.304 Å		1.92 Å/pix.
x 224 pix.
= 430.304 Å		1.92 Å/pix.
x 224 pix.
= 430.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 1.1
Minimum - Maximum-2.10768795 - 5.43387604
Average (Standard dev.)0.00302596 (±0.15822503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 430.30402 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.9211.9211.921
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z430.304430.304430.304
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-2.1085.4340.003

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Supplemental data

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Sample components

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Entire : Core NuRD complex (MTA1:HDAC1:RBBP4)

EntireName: Core NuRD complex (MTA1:HDAC1:RBBP4)
Components
  • Sample: Core NuRD complex (MTA1:HDAC1:RBBP4)
  • Ligand: MTA1
  • Ligand: HDAC1
  • Ligand: RBBP4

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Supramolecule #1000: Core NuRD complex (MTA1:HDAC1:RBBP4)

SupramoleculeName: Core NuRD complex (MTA1:HDAC1:RBBP4) / type: sample / ID: 1000 / Details: Dimer / Oligomeric state: 2 / Number unique components: 3
Molecular weightExperimental: 300 KDa / Theoretical: 300 KDa / Method: SEC-MALS

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Macromolecule #1: MTA1

MacromoleculeName: MTA1 / type: ligand / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: HEK293F / Recombinant plasmid: pcDNA3

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Macromolecule #2: HDAC1

MacromoleculeName: HDAC1 / type: ligand / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: HEK293F / Recombinant plasmid: pcDNA3

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Macromolecule #3: RBBP4

MacromoleculeName: RBBP4 / type: ligand / ID: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: HEK293F / Recombinant plasmid: pcDNA3

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris/HCl (pH 7.5), 40 mM NaCl
StainingType: NEGATIVE / Details: 2% uranyl acetate for 1 min
GridDetails: Prepared by glow discharging carbon coated copper 300 mesh grids (agar scientific) at 10 mA for 30 seconds
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2010F
DateJul 22, 2015
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 308
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL

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Image processing

DetailsThe particles were selected using an automatic selection program.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 17841
Final two d classificationNumber classes: 32
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4bkx


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera
DetailsFit in map (Chimera)
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

5fxy


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera
DetailsFit in map (Chimera)
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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