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Yorodumi- PDB-4yym: Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yym | ||||||
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Title | Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysine peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / Bromodomain-butyryllysine complex | ||||||
Function / homology | Function and homology information negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / midbrain development / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity ...negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / midbrain development / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / MLL1 complex / positive regulation of transcription initiation by RNA polymerase II / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / RNA polymerase II core promoter sequence-specific DNA binding / lipoxygenase pathway / negative regulation of ubiquitin-dependent protein catabolic process / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / linoleic acid metabolic process / histone acetyltransferase / lysine-acetylated histone binding / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / regulation of signal transduction by p53 class mediator / mRNA transcription by RNA polymerase II / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / p53 binding / protein polyubiquitination / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / kinase activity / peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / sequence-specific DNA binding / protein autophosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Tang, Y. / Bellon, S. / Cochran, A.G. / Poy, F. | ||||||
Citation | Journal: Structure / Year: 2015 Title: A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Authors: Flynn, E.M. / Huang, O.W. / Poy, F. / Oppikofer, M. / Bellon, S.F. / Tang, Y. / Cochran, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yym.cif.gz | 128.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yym.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yym_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 4yym_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 4yym_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 4yym_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/4yym ftp://data.pdbj.org/pub/pdb/validation_reports/yy/4yym | HTTPS FTP |
-Related structure data
Related structure data | 4yy4C 4yy6C 4yydC 4yygC 4yyhC 4yyiC 4yyjC 4yykC 4yynC 1eqfS 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
#1: Protein | Mass: 16576.604 Da / Num. of mol.: 2 / Fragment: bromodomain (UNP residues 1497-1638) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21675 #2: Protein/peptide | | Mass: 1114.279 Da / Num. of mol.: 1 / Fragment: N-terminal tail (UNP residues 2-12) / Source method: obtained synthetically / Details: lysine residues butyrylated / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805 #3: Chemical | ChemComp-CA / | #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: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M calcium chloride, 20 w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 8, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 50570 / % possible obs: 99.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.051 / Χ2: 1.034 / Net I/av σ(I): 29.188 / Net I/σ(I): 12.4 / Num. measured all: 302465 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EQF Resolution: 1.5→29.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.234 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 85.06 Å2 / Biso mean: 30.377 Å2 / Biso min: 15.27 Å2
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Refinement step | Cycle: final / Resolution: 1.5→29.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.498→1.537 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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