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- PDB-3hmh: Crystal structure of the second bromodomain of human TBP-associat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hmh | ||||||
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Title | Crystal structure of the second bromodomain of human TBP-associated factor RNA polymerase 1-like (TAF1L) | ||||||
![]() | Transcription initiation factor TFIID 210 kDa subunit | ||||||
![]() | TRANSCRIPTION / MGC134910 / TAF2A2 / Structural Genomics Consortium / SGC / Bromodomain / Cell cycle / Disulfide bond / DNA-binding / Nucleus / Transcription regulation | ||||||
Function / homology | ![]() male meiotic nuclear division / RNA polymerase II general transcription initiation factor binding / 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 factor TFIID complex ...male meiotic nuclear division / RNA polymerase II general transcription initiation factor binding / 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 factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / lysine-acetylated histone binding / Regulation of TP53 Activity through Phosphorylation / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Filippakopoulos, P. / Picaud, S. / Keates, T. / Zhang, Y. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. ...Filippakopoulos, P. / Picaud, S. / Keates, T. / Zhang, Y. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / 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 | ![]() | 44.5 KB | Display | ![]() |
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PDB format | ![]() | 30 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.1 KB | Display | ![]() |
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Full document | ![]() | 419.1 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxbSC ![]() 2oo1SC ![]() 2ossSC ![]() 2ouoSC ![]() 2rfjSC ![]() 3d7cSC ![]() 3daiSC ![]() 3dwySC ![]() 3gg3C ![]() 3hmeC ![]() 3hmfC ![]() 3i3jC ![]() 3iu5C ![]() 3iu6C ![]() 3lxjC ![]() 3mb3C ![]() 3mb4C ![]() 3mqmC ![]() 3nxbC ![]() 3p1cC ![]() 3p1dC ![]() 3q2eC ![]() 3rcwC ![]() 3tlpC ![]() 3uv2C ![]() 3uv4C ![]() 3uv5C ![]() 3uvdC ![]() 3uvwC ![]() 3uvxC ![]() 3uvyC ![]() 3uw9C 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18023.252 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1523-1651 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.17 % / Mosaicity: 0.78 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15w/v PEG_3350, 0.17M ammonium_sulfate, 15w/v glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→28.15 Å / Num. all: 9764 / Num. obs: 9764 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1392 / Rsym value: 0.687 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 56.99 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY Resolution: 2.05→28.15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.838 / SU B: 11.214 / SU ML: 0.135 / SU R Cruickshank DPI: 0.199 / SU Rfree: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.38 Å2 / Biso mean: 18.147 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→28.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 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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