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Basic information
Entry | Database: PDB / ID: 5fxy | ||||||
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Title | Structure of the human RBBP4:MTA1(464-546) complex | ||||||
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![]() | TRANSCRIPTION / TRANSCRIPTION REPRESSION COMPLEX METASTASIS ASSOCIATED COMPLEX MTA1 RBBP4 RBBP7 HISTONE BINDING PROTEIN | ||||||
Function / homology | ![]() CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / positive regulation of protein autoubiquitination / Polo-like kinase mediated events / response to ionizing radiation / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / Sin3-type complex / entrainment of circadian clock by photoperiod / Transcriptional Regulation by E2F6 / locomotor rhythm / RNA Polymerase I Transcription Initiation / histone deacetylase complex / SUMOylation of transcription factors / G0 and Early G1 / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / brain development / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / double-strand break repair / nucleosome assembly / nuclear envelope / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / DNA replication / RNA polymerase II-specific DNA-binding transcription factor binding / microtubule / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
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![]() | Millard, C.J. / Varma, N. / Fairall, L. / Schwabe, J.W.R. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 351.8 KB | Display | ![]() |
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PDB format | ![]() | 289.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3399C ![]() 6g16C ![]() 4pc0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
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Components
#1: Protein | Mass: 47709.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 9773.559 Da / Num. of mol.: 4 / Fragment: RESIDUES 464-546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.21 M AMMONIUM CITRATE AND 19% PEG 3350, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Jul 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→95.3 Å / Num. obs: 35054 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.2→3.34 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4PC0 Resolution: 3.2→95.29 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.844 / SU B: 35.296 / SU ML: 0.57 / Cross valid method: THROUGHOUT / ESU R Free: 0.611 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.709 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→95.29 Å
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