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Yorodumi- PDB-3qzt: Crystal Structure of BPTF bromo in complex with histone H4K16ac -... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qzt | ||||||
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Title | Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form II | ||||||
Components |
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Keywords | TRANSCRIPTION/NUCLEAR PROTEIN / protein-peptide complex / all alpha helix / transcription / histone h4 / nuclear / TRANSCRIPTION-NUCLEAR PROTEIN complex | ||||||
Function / homology | Function and homology information NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / negative regulation of megakaryocyte differentiation / embryonic placenta development / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / negative regulation of megakaryocyte differentiation / embryonic placenta development / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / methylated histone binding / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / cellular response to nerve growth factor stimulus / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / brain development / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / cell body / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Li, H. / Ruthenburg, A.J. / Patel, D.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2011 Title: Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions. Authors: Ruthenburg, A.J. / Li, H. / Milne, T.A. / Dewell, S. / McGinty, R.K. / Yuen, M. / Ueberheide, B. / Dou, Y. / Muir, T.W. / Patel, D.J. / Allis, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qzt.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qzt.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 3qzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qzt_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 3qzt_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 3qzt_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 3qzt_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/3qzt ftp://data.pdbj.org/pub/pdb/validation_reports/qz/3qzt | HTTPS FTP |
-Related structure data
Related structure data | 3qzsC 3qzvC 2f6jS 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: 13443.338 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 2924-3037) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2 / References: UniProt: Q12830 |
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#2: Protein/peptide | Mass: 1183.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: P62805 |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.1 Å3/Da / Density % sol: 41.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% (W/V) PEGMME 2K, 20% Glycerol and 0.2 M KCl, 0.1 M Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→20 Å / Num. obs: 19449 / % possible obs: 98.1 % / Rmerge(I) obs: 0.073 / Χ2: 1.271 / Net I/σ(I): 14.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2F6J Resolution: 1.5→19.86 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1984 / WRfactor Rwork: 0.1638 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8994 / SU B: 2.415 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0746 / SU Rfree: 0.0779 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 265.65 Å2 / Biso mean: 18.07 Å2 / Biso min: 6.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 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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