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Yorodumi- PDB-2x4y: Molecular basis of Histone H3K36me3 recognition by the PWWP domai... -
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-Basic information
Entry | Database: PDB / ID: 2x4y | ||||||
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Title | Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. | ||||||
Components |
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Keywords | TRANSCRIPTION / METAL-BINDING / ZINC-FINGER / CHROMATIN REGULATOR / TRANSCRIPTION REGULATION / NUCLEOSOME | ||||||
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 / Regulation of TP53 Activity through Acetylation / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication ...acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / Chromatin modifying enzymes / Regulation of TP53 Activity through Acetylation / 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 / 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 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / 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 / Resolution: 1.7 Å | ||||||
Authors | Vezzoli, A. / Bonadies, N. / Allen, M.D. / Freund, S.M.V. / Santiveri, C.M. / Kvinlaug, B. / Huntly, B.J.P. / Gottgens, B. / Bycroft, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Molecular Basis of Histone H3K36Me3 Recognition by the Pwwp Domain of Brpf1. Authors: Vezzoli, A. / Bonadies, N. / Allen, M.D. / Freund, S.M.V. / Santiveri, C.M. / Kvinlaug, B. / Huntly, B.J.P. / Gottgens, B. / Bycroft, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x4y.cif.gz | 251.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x4y.ent.gz | 212 KB | Display | PDB format |
PDBx/mmJSON format | 2x4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4y ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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8 |
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Unit cell |
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-Components
#1: Protein | Mass: 15249.579 Da / Num. of mol.: 8 / Fragment: BRPF1 PWWP DOMAIN, RESIDUES 1076-1205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P55201 #2: Protein/peptide | Mass: 2330.777 Da / Num. of mol.: 8 / Fragment: RESIDUES 23-43 / Source method: obtained synthetically / Details: TRIMETHYLATED AT POSITION 36 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q71DI3 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | LYSINE 36 IS TRIMETHYLA | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.08 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.85 Å / Num. obs: 1418928 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 23.91 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.771 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 22.94 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.898 Å2 / ksol: 0.397 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→24.771 Å
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Refine LS restraints |
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LS refinement shell |
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