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- PDB-4yym: Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysin... -
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Basic information
Entry | Database: PDB / ID: 4yym | ||||||
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Title | Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysine peptide | ||||||
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![]() | PROTEIN BINDING / Bromodomain-butyryllysine complex | ||||||
Function / homology | ![]() 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 / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...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 / 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 / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / negative regulation of megakaryocyte differentiation / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / histone acetyltransferase activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / RNA polymerase II preinitiation complex assembly / Deposition of new CENPA-containing nucleosomes at the centromere / histone acetyltransferase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / TBP-class protein binding / RNA Polymerase I Promoter Opening / negative regulation of ubiquitin-dependent protein catabolic process / 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 / regulation of signal transduction by p53 class mediator / Defective pyroptosis / HDACs deacetylate histones / nuclear receptor binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / peptidyl-threonine phosphorylation / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / protein polyubiquitination / structural constituent of chromatin / cellular response to UV / nucleosome / nucleosome assembly / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / kinase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Tang, Y. / Bellon, S. / Cochran, A.G. / Poy, F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.6 KB | Display | ![]() |
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PDB format | ![]() | 98.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yy4C ![]() 4yy6C ![]() 4yydC ![]() 4yygC ![]() 4yyhC ![]() 4yyiC ![]() 4yyjC ![]() 4yykC ![]() 4yynC ![]() 1eqfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #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.) ![]() #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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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