[English] 日本語
Yorodumi- PDB-5iok: Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iok | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / crotonylation / crotonyllysine / epigenetics / reader / histone H3 / H3K9cr | ||||||
Function / homology | Function and homology information NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / transcription factor TFIIF complex / Ino80 complex / mediator complex / replication fork protection complex / Oxidative Stress Induced Senescence / SWI/SNF complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / CENP-A containing nucleosome / intracellular copper ion homeostasis / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / aerobic respiration / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription by RNA polymerase II / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Andrews, F.H. / Kuateladze, T.G. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: The Taf14 YEATS domain is a reader of histone crotonylation. Authors: Andrews, F.H. / Shinsky, S.A. / Shanle, E.K. / Bridgers, J.B. / Gest, A. / Tsun, I.K. / Krajewski, K. / Shi, X. / Strahl, B.D. / Kutateladze, T.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5iok.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5iok.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 5iok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iok_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5iok_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 5iok_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 5iok_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/5iok ftp://data.pdbj.org/pub/pdb/validation_reports/io/5iok | HTTPS FTP |
-Related structure data
Related structure data | 5d7eS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16180.497 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Escherichia coli (E. coli) / References: UniProt: P35189 | ||
---|---|---|---|
#2: Protein/peptide | ( Mass: 885.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide is N-terminally acetylated / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61830*PLUS | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 44% PEG600 (v/v) and 0.2 M citric acid (pH 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→32.65 Å / Num. obs: 9584 / % possible obs: 97.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.22→2.26 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 72.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5d7e Resolution: 2.22→32.648 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.42 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→32.648 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 43.6113 Å / Origin y: 13.0749 Å / Origin z: 2.021 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |