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Yorodumi- PDB-4qyl: Crystal Structure of the human BRPF1 bromodomain in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 4qyl | ||||||
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Title | Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac 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 / 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 / Regulation of TP53 Activity through Acetylation / HCMV Late Events / HDACs deacetylate histones / Metalloprotease DUBs / RMTs methylate histone arginines ...acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HCMV Late Events / HDACs deacetylate histones / Metalloprotease DUBs / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / UCH proteinases / nucleosome / HATs acetylate histones / Ub-specific processing proteases / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / DNA binding / extracellular exosome / 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: 1.8 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 | 4qyl.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qyl.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/4qyl ftp://data.pdbj.org/pub/pdb/validation_reports/qy/4qyl | HTTPS FTP |
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-Related structure data
Related structure data | 4qydC 3rcwS 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 1 - 117 / Label seq-ID: 1 - 117
NCS ensembles :
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-Components
#1: Protein | Mass: 13720.686 Da / Num. of mol.: 4 / 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) / Strain (production host): Rosetta2DE3pLysS / References: UniProt: P55201 #2: Protein/peptide | Mass: 1217.361 Da / Num. of mol.: 4 / Fragment: histone H2AK5ac peptide (UNP residues 2-13) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0C0S8 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M NH4SO4, 0.1 M MES monohydrate, pH 6.5, 30% w/v polyethylene glycol monomethyl ether (PEG) 5000, 1% propylene glycol, 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 Å |
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: 1.8→41.02 Å / Num. all: 48421 / Num. obs: 48421 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.04 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3RCW Resolution: 1.8→41.02 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.095 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.149 / 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: 20.965 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→41.02 Å
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Refine LS restraints |
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