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Yorodumi- PDB-3uv5: Crystal Structure of the tandem bromodomains of human Transcripti... -
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-Basic information
Entry | Database: PDB / ID: 3uv5 | ||||||
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Title | Crystal Structure of the tandem bromodomains of human Transcription initiation factor TFIID subunit 1 (TAF1) | ||||||
Components | Transcription initiation factor TFIID subunit 1 | ||||||
Keywords | TRANSCRIPTION / Tandem bromodomain / TAF1 / Cell cycle gene 1 protein / TBP-associated factor 250 kDa / Transcription initiation factor TFIID 250 kDa subunit / TFII-250 / Structural Genomics Consortium / SGC | ||||||
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 / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex ...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 / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 / ubiquitin conjugating enzyme activity / MLL1 complex / transcription initiation at RNA polymerase I promoter / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / negative regulation of ubiquitin-dependent protein catabolic process / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / regulation of signal transduction by p53 class mediator / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / protein polyubiquitination / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / protein heterodimerization activity / negative regulation of gene expression / protein phosphorylation / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å | ||||||
Authors | Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2012 Title: Histone recognition and large-scale structural analysis of the human bromodomain family. Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uv5.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uv5.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 3uv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/3uv5 ftp://data.pdbj.org/pub/pdb/validation_reports/uv/3uv5 | HTTPS FTP |
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-Related structure data
Related structure data | 2nxbC 2oo1SC 2ossSC 2ouoSC 2rfjC 3d7cSC 3daiSC 3dwySC 3gg3SC 3hmeC 3hmfC 3hmhSC 3i3jC 3iu5C 3iu6C 3lxjC 3mb3C 3mb4C 3mqmC 3nxbC 3p1cC 3p1dC 3q2eC 3rcwC 3tlpC 3uv2C 3uv4C 3uvdC 3uvwC 3uvxC 3uvyC 3uw9C 2grcS 3g0lS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30968.256 Da / Num. of mol.: 1 / Fragment: unp residues 1373-1635 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BA2R, CCG1, CCGS, TAF1, TAF2A / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 References: UniProt: P21675, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-TRS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density meas: 70.03 Mg/m3 / Density % sol: 70.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1M Tris-HCl, 1.1M (NH4)2SO4, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.5 % / Av σ(I) over netI: 6 / Number: 216346 / Rsym value: 0.092 / D res high: 2.03 Å / D res low: 34.482 Å / Num. obs: 33176 / % possible obs: 99.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.03→34.482 Å / Num. all: 33444 / Num. obs: 33176 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 11.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 41.69 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3 Resolution: 2.03→34.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2303 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.861 / SU B: 6.273 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1279 / SU Rfree: 0.1296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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: 183.28 Å2 / Biso mean: 40.9279 Å2 / Biso min: 15.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→34.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.083 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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