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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3399 | |||||||||
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Title | Structure of the core NuRD complex (MTA1:HDAC1:RBBP4) | |||||||||
![]() | Structure of the core NuRD complex: MTA1:HDAC1:RBBP4 | |||||||||
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![]() | Transcription / HDAC1 / MTA1 / RBBP4 / Chromatin / Histone Deacetylase / Metastasis associated protein / Histone binding protein | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
![]() | Millard CJ / Saleh A / Morris K / Fairall L / Smith CJ / Schwabe JWR | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.9 KB 10.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.3 KB | Display | ![]() |
Images | ![]() | 122.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 227.3 KB | Display | ![]() |
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Full document | ![]() | 226.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Structure of the core NuRD complex: MTA1:HDAC1:RBBP4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.921 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Core NuRD complex (MTA1:HDAC1:RBBP4)
Entire | Name: Core NuRD complex (MTA1:HDAC1:RBBP4) |
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Components |
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-Supramolecule #1000: Core NuRD complex (MTA1:HDAC1:RBBP4)
Supramolecule | Name: Core NuRD complex (MTA1:HDAC1:RBBP4) / type: sample / ID: 1000 / Details: Dimer / Oligomeric state: 2 / Number unique components: 3 |
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Molecular weight | Experimental: 300 KDa / Theoretical: 300 KDa / Method: SEC-MALS |
-Macromolecule #1: MTA1
Macromolecule | Name: MTA1 / type: ligand / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: HEK293F / Recombinant plasmid: pcDNA3 |
-Macromolecule #2: HDAC1
Macromolecule | Name: HDAC1 / type: ligand / ID: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: HEK293F / Recombinant plasmid: pcDNA3 |
-Macromolecule #3: RBBP4
Macromolecule | Name: RBBP4 / type: ligand / ID: 3 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: HEK293F / Recombinant plasmid: pcDNA3 |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.5 / Details: 20 mM Tris/HCl (pH 7.5), 40 mM NaCl |
Staining | Type: NEGATIVE / Details: 2% uranyl acetate for 1 min |
Grid | Details: Prepared by glow discharging carbon coated copper 300 mesh grids (agar scientific) at 10 mA for 30 seconds |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | JEOL 2010F |
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Date | Jul 22, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 308 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Specimen holder model: JEOL |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: ![]() |
Details | Fit in map (Chimera) |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: ![]() |
Details | Fit in map (Chimera) |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |