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Yorodumi- PDB-5ffv: Crystal structure of the bromodomain of human BRPF1 in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 5ffv | ||||||
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Title | Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / Peregrin / MOZ-MORF complex | ||||||
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 / epigenetic regulation of gene expression / Regulation of TP53 Activity through Acetylation / telomere organization / RNA Polymerase I Promoter Opening ...acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / Chromatin modifying enzymes / epigenetic regulation of gene expression / Regulation of TP53 Activity through Acetylation / telomere organization / 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 / gene expression / 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 / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Tallant, C. / Nunez-Alonso, G. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone peptide Authors: Tallant, C. / Nunez-Alonso, G. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ffv.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ffv.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ffv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/5ffv ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ffv | HTTPS FTP |
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-Related structure data
Related structure data | 4lc2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13703.698 Da / Num. of mol.: 2 / Fragment: UNP residues 626-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201 #2: Protein/peptide | Mass: 1202.384 Da / Num. of mol.: 2 / Fragment: UNP residues 10-20 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: K7EMV3, UniProt: P68431*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.77 % / Description: Rod |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350, 0.2 M MgCl2, 0.1 M bis-tris pH 5.5 / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→29.73 Å / Num. all: 67343 / Num. obs: 67343 / % possible obs: 98.6 % / Redundancy: 11.1 % / Biso Wilson estimate: 13.37 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.027 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.5 / % possible all: 90.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LC2 Resolution: 1.3→29.73 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.364 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / 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: 18.865 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→29.73 Å
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