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Yorodumi- PDB-3mo8: PWWP Domain of Human Bromodomain and PHD finger-containing protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mo8 | ||||||
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Title | PWWP Domain of Human Bromodomain and PHD finger-containing protein 1 In Complex with Trimethylated H3K36 Peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / Peregrin / Protein BR140 / histone H3 acetylation / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / Chromatin modifying enzymes / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / Chromatin modifying enzymes / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Regulation of TP53 Activity through Acetylation / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å | ||||||
Authors | Lam, R. / Zeng, H. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Structural and Histone Binding Ability Characterizations of Human PWWP Domains. Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Amaya, M.F. / Xu, C. / Dombrovski, L. / Qiu, W. / Wang, Y. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mo8.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mo8.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/3mo8 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3mo8 | HTTPS FTP |
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-Related structure data
Related structure data | 3eaeC 3l42SC 3llrC 3lyiC 3pfsC 3pmiC 3qbyC 3qj6C 3qkjC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | As per the authors the biological assembly is a monomer |
-Components
#1: Protein | Mass: 15076.455 Da / Num. of mol.: 1 / Fragment: UNP residues 1079-1207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BR140, BRPF1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: P55201 |
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#2: Protein/peptide | Mass: 1356.615 Da / Num. of mol.: 1 / Fragment: UNP residue 31-42 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3, UniProt: Q16695*PLUS |
#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: 2.63 Å3/Da / Density meas: 2.63 Mg/m3 / Density % sol: 53.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 3.5M sodium formate, 0.1M Tris-HCl pH8.5, H3K36me3 peptide, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→50 Å / Num. obs: 19545 / % possible obs: 99.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3L42 Resolution: 1.69→36.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.05 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.093 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.748 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→36.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.735 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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