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Yorodumi- PDB-7n42: Crystal structure of the tandem bromodomain of human TAF1 (TAF1-T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n42 | ||||||
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Title | Crystal structure of the tandem bromodomain of human TAF1 (TAF1-T) bound to ZS1-681 | ||||||
Components | Transcription initiation factor TFIID subunit 1 | ||||||
Keywords | GENE REGULATION / Bromodomain / TAF1 / non-BET / BET / kinase inhibitor / ATR / dual BRD-kinase / transferase | ||||||
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 / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of ubiquitin-dependent protein catabolic process / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Karim, M.R. / Schonbrunn, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the tandem bromodomain of human TAF1 (TAF1-T) bound to ZS1-681 Authors: Karim, M.R. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n42.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n42.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 7n42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/7n42 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/7n42 | HTTPS FTP |
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-Related structure data
Related structure data | 7k03S 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: 30968.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Plasmid: pNIC28.Bsa4 / Production host: Escherichia coli (E. coli) References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-06M / | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 26, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 24715 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.18 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Χ2: 0.836 / Net I/σ(I): 9.6 / Num. measured all: 158462 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7K03 Resolution: 1.9→36.59 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.57 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.35 Å2 / Biso mean: 25.8183 Å2 / Biso min: 10.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→36.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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