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Yorodumi- PDB-6ew6: Crystal structure of the BCL6 BTB domain in complex with anilinop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ew6 | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with anilinopyrimidine ligand | ||||||
Components | B-cell lymphoma 6 protein | ||||||
Keywords | TRANSFERASE / KINASE | ||||||
Function / homology | Function and homology information regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation ...regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation / plasma cell differentiation / paraspeckles / germinal center formation / pyramidal neuron differentiation / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / T-helper 2 cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / regulation of cell differentiation / negative regulation of cellular senescence / erythrocyte development / Rho protein signal transduction / regulation of immune response / heterochromatin formation / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / protein localization / cell morphogenesis / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.39 Å | ||||||
Authors | Robb, G. / Ferguson, A. / Hargreaves, D. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Development of a Novel B-Cell Lymphoma 6 (BCL6) PROTAC To Provide Insight into Small Molecule Targeting of BCL6. Authors: McCoull, W. / Cheung, T. / Anderson, E. / Barton, P. / Burgess, J. / Byth, K. / Cao, Q. / Castaldi, M.P. / Chen, H. / Chiarparin, E. / Carbajo, R.J. / Code, E. / Cowan, S. / Davey, P.R. / ...Authors: McCoull, W. / Cheung, T. / Anderson, E. / Barton, P. / Burgess, J. / Byth, K. / Cao, Q. / Castaldi, M.P. / Chen, H. / Chiarparin, E. / Carbajo, R.J. / Code, E. / Cowan, S. / Davey, P.R. / Ferguson, A.D. / Fillery, S. / Fuller, N.O. / Gao, N. / Hargreaves, D. / Howard, M.R. / Hu, J. / Kawatkar, A. / Kemmitt, P.D. / Leo, E. / Molina, D.M. / O'Connell, N. / Petteruti, P. / Rasmusson, T. / Raubo, P. / Rawlins, P.B. / Ricchiuto, P. / Robb, G.R. / Schenone, M. / Waring, M.J. / Zinda, M. / Fawell, S. / Wilson, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ew6.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ew6.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ew6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/6ew6 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/6ew6 | HTTPS FTP |
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-Related 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: 14183.435 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P41182 |
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#2: Chemical | ChemComp-C0H / ~{ |
#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: 2.04 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→36.51 Å / Num. obs: 22114 / % possible obs: 96.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.17 Å2 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.39→1.47 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Resolution: 1.39→14.93 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.069
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Displacement parameters | Biso mean: 22.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→14.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.39→1.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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