+Open data
-Basic information
Entry | Database: PDB / ID: 4pbz | ||||||
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Title | Structure of the human RbAp48-MTA1(670-695) complex | ||||||
Components |
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Keywords | CELL CYCLE / NuRD / sub-complex | ||||||
Function / homology | Function and homology information CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / 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 ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / 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 / Polo-like kinase mediated events / positive regulation of protein autoubiquitination / negative regulation of gene expression, epigenetic / response to ionizing radiation / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / 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 / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / 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 / brain development / circadian regulation of gene expression / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / transcription corepressor activity / double-strand break repair / nuclear envelope / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / transcription coactivator activity / chromatin remodeling / cell cycle / 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 / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Murthy, A. / Pei, X.Y. / Watson, A.A. / Silva, A.P.G. / Mackay, J.P. / Laue, E.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Insight into the architecture of the NuRD complex: Structure of the RbAp48-MTA1 sub-complex. Authors: Alqarni, S.S. / Murthy, A. / Zhang, W. / Przewloka, M.R. / Silva, A.P. / Watson, A.A. / Lejon, S. / Pei, X.Y. / Smits, A.H. / Kloet, S.L. / Wang, H. / Shepherd, N.E. / Stokes, P.H. / Blobel, ...Authors: Alqarni, S.S. / Murthy, A. / Zhang, W. / Przewloka, M.R. / Silva, A.P. / Watson, A.A. / Lejon, S. / Pei, X.Y. / Smits, A.H. / Kloet, S.L. / Wang, H. / Shepherd, N.E. / Stokes, P.H. / Blobel, G.A. / Vermeulen, M. / Glover, D.M. / Mackay, J.P. / Laue, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pbz.cif.gz | 183 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pbz.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/4pbz ftp://data.pdbj.org/pub/pdb/validation_reports/pb/4pbz | HTTPS FTP |
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-Related structure data
Related structure data | 4pbyC 4pc0C 2xu7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47709.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Plasmid: PFBDM / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028 |
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#2: Protein/peptide | Mass: 2963.462 Da / Num. of mol.: 1 / Fragment: Residues 653-678 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13330 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v 2-Methyl-2,4-pentanediol (MPD), 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0. ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v 2-Methyl-2,4-pentanediol (MPD), 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, and 0.1 M MES/imidazole pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 14, 2012 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.15→33.6 Å / Num. obs: 26112 / % possible obs: 97.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 39.99 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.035 / Net I/σ(I): 13 / Num. measured all: 94637 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XU7 Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.027 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 168.65 Å2 / Biso mean: 61.125 Å2 / Biso min: 20.16 Å2
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Refinement step | Cycle: final / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.205 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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