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- 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) | ||||||
![]() | Transcription initiation factor TFIID subunit 1 | ||||||
![]() | 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 | ![]() 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 / 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 / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / negative regulation of ubiquitin-dependent protein catabolic process / 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 / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.8 KB | Display | ![]() |
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PDB format | ![]() | 95.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.6 KB | Display | ![]() |
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Full document | ![]() | 442.3 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( 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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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.) ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() | |||||||||
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Phasing MR | Rfactor: 41.69 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() 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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