+Open data
-Basic information
Entry | Database: PDB / ID: 5d7e | |||||||||||||||
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Title | Crystal structure of Taf14 YEATS domain in complex with H3K9ac | |||||||||||||||
Components |
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Keywords | NUCLEAR PROTEIN / acetylation histone YEATS reader | |||||||||||||||
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 / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Ino80 complex / mediator complex / transcription factor TFIIF complex / replication fork protection complex ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Ino80 complex / mediator complex / transcription factor TFIIF complex / replication fork protection complex / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / CENP-A containing nucleosome / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription by RNA polymerase II / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||||||||
Authors | Andrews, F.H. / Shanle, E.K. / Strahl, B.D. / Kutateladze, T.G. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Genes Dev. / Year: 2015 Title: Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response. Authors: Shanle, E.K. / Andrews, F.H. / Meriesh, H. / McDaniel, S.L. / Dronamraju, R. / DiFiore, J.V. / Jha, D. / Wozniak, G.G. / Bridgers, J.B. / Kerschner, J.L. / Krajewski, K. / Martin, G.M. / ...Authors: Shanle, E.K. / Andrews, F.H. / Meriesh, H. / McDaniel, S.L. / Dronamraju, R. / DiFiore, J.V. / Jha, D. / Wozniak, G.G. / Bridgers, J.B. / Kerschner, J.L. / Krajewski, K. / Martin, G.M. / Morrison, A.J. / Kutateladze, T.G. / Strahl, B.D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d7e.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d7e.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 5d7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/5d7e ftp://data.pdbj.org/pub/pdb/validation_reports/d7/5d7e | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16026.331 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 | ||||
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#2: Protein/peptide | Mass: 904.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61830*PLUS | ||||
#3: Chemical | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M sodium citrate and 48% PEG600 (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.98 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Nov 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→56.52 Å / Num. obs: 15763 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→56 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
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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: 1.9→56 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 43.7059 Å / Origin y: 13.737 Å / Origin z: 1.3062 Å
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Refinement TLS group | Selection details: all |