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Yorodumi- PDB-4qyd: Crystal Structure of the human BRPF1 bromodomain in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 4qyd | ||||||
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Title | Crystal Structure of the human BRPF1 bromodomain in complex with a histone H4K12ac peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / bromodomain-PHD finger protein 1 (BRPF1) / histone acetyltransferase (HAT) / monocytic leukemia zinc-finger (MOZ) / epigenetics / chromatin reader / bromodomain / histone post-transcriptional modification (PTM) reader domain / histone H4 acetylated at lysine 14 / acetyllysine / nucleus | ||||||
Function / homology | Function and homology information acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / negative regulation of megakaryocyte differentiation / 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 / Regulation of TP53 Activity through Acetylation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / 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 / 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 / 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 / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / RNA 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: 1.94 Å | ||||||
Authors | Lubula, M.Y. / Glass, K.C. | ||||||
Citation | Journal: Febs Lett. / Year: 2014 Title: Structural insights into recognition of acetylated histone ligands by the BRPF1 bromodomain. Authors: Lubula, M.Y. / Eckenroth, B.E. / Carlson, S. / Poplawski, A. / Chruszcz, M. / Glass, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qyd.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qyd.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/4qyd ftp://data.pdbj.org/pub/pdb/validation_reports/qy/4qyd | HTTPS FTP |
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-Related structure data
Related structure data | 4qylC 2d9eS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13720.686 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 629-742) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BR140, BRPF1 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201 |
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#2: Protein/peptide | Mass: 1316.555 Da / Num. of mol.: 1 / Fragment: histone H4K12ac peptide (UNP residues 5-18) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805 |
#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: 4.05 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: 0.1 M HEPES, pH 7.5, 10% w/v polyethylene glycol (PEG) 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2013 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→34.43 Å / Num. obs: 18780 / % possible obs: 99.9 % / Observed criterion σ(I): 14.66 / Redundancy: 27.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 25.84 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 27.2 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 14.66 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D9E Resolution: 1.94→34.43 Å / SU ML: 0.12 / σ(F): 1.37 / Phase error: 18.93 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→34.43 Å
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Refine LS restraints |
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LS refinement shell |
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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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