[English] 日本語
![](img/lk-miru.gif)
- PDB-7aoa: Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7aoa | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex | ||||||||||||
![]() |
| ||||||||||||
![]() | TRANSCRIPTION / Deacetylase / Complex | ||||||||||||
Function / homology | ![]() Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / satellite DNA binding / CAF-1 complex / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / ventricular cardiac muscle tissue development ...Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / satellite DNA binding / CAF-1 complex / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / ventricular cardiac muscle tissue development / fungiform papilla formation / negative regulation of androgen receptor signaling pathway / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / endoderm development / DNA replication-dependent chromatin assembly / maternal behavior / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / NuRD complex / DNA methylation-dependent heterochromatin formation / siRNA binding / protein deacetylation / ESC/E(Z) complex / Transcription of E2F targets under negative control by DREAM complex / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / positive regulation of protein autoubiquitination / histone deacetylase / C2H2 zinc finger domain binding / methyl-CpG binding / protein lysine deacetylase activity / positive regulation of signaling receptor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / negative regulation of gene expression, epigenetic / positive regulation of oligodendrocyte differentiation / histone deacetylase activity / response to ionizing radiation / Sin3-type complex / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / cellular response to platelet-derived growth factor stimulus / Notch-HLH transcription pathway / eyelid development in camera-type eye / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / E-box binding / entrainment of circadian clock by photoperiod / odontogenesis of dentin-containing tooth / locomotor rhythm / RNA Polymerase I Transcription Initiation / SUMOylation of transcription factors / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / cellular response to organic cyclic compound / G0 and Early G1 / NF-kappaB binding / positive regulation of Wnt signaling pathway / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / embryonic organ development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Nuclear events stimulated by ALK signaling in cancer / heterochromatin / Cyclin E associated events during G1/S transition / response to mechanical stimulus / MECP2 regulates neuronal receptors and channels / core promoter sequence-specific DNA binding / negative regulation of intrinsic apoptotic signaling pathway / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of canonical NF-kappaB signal transduction / nucleosome binding / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / transcription repressor complex / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / negative regulation of cell migration / response to nutrient levels / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / Deactivation of the beta-catenin transactivating complex / HDACs deacetylate histones / hippocampus development / promoter-specific chromatin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / circadian regulation of gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19.4 Å | ||||||||||||
![]() | Millard, C.J. / Fairall, L. / Ragan, T.J. / Savva, C.G. / Schwabe, J.W.R. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: The topology of chromatin-binding domains in the NuRD deacetylase complex. Authors: Christopher J Millard / Louise Fairall / Timothy J Ragan / Christos G Savva / John W R Schwabe / ![]() Abstract: Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated ...Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Using biochemical approaches and cryo-electron microscopy, we have determined how three chromatin-binding domains (MTA1-BAH, MBD2/3 and RBBP4/7) are assembled in relation to the core complex so as to facilitate interaction of the complex with the genome. We observe a striking arrangement of the BAH domains suggesting a potential mechanism for binding to di-nucleosomes. We also find that the WD40 domains from RBBP4 are linked to the core with surprising flexibility that is likely important for chromatin engagement. A single MBD2 protein binds asymmetrically to the dimerisation interface of the complex. This symmetry mismatch explains the stoichiometry of the complex. Finally, our structures suggest how the holo-NuRD might assemble on a di-nucleosome substrate. | ||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 466.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 365.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 64.5 KB | Display | |
Data in CIF | ![]() | 102.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11839MC ![]() 7ao8C ![]() 7ao9C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 4 types, 7 molecules CDAEBFG
#1: Protein | Mass: 43323.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 80904.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 55178.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 47709.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 3 types, 8 molecules ![](data/chem/img/IHP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-K / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Extended NuRD deacetylase complex containing two copies of MTA1, HDAC1 and RBBP4 and a single copy of MBD2 Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.34 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: 40 mA for 120 sec / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot for 3 seconds, blot force 10 |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 129629 X / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 100 K |
Image recording | Average exposure time: 60 sec. / Electron dose: 34 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1902 |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 55799 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 19.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10066 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||
Atomic model building |
|