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Yorodumi- PDB-5n1z: Crystal structure of the BCL6 BTB domain in complex with pyrazolo... -
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-Basic information
Entry | Database: PDB / ID: 5n1z | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with pyrazolo-pyrimidine macrocyclic 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 mast cell cytokine production / regulation of germinal center formation / plasma cell differentiation ...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 mast cell cytokine production / regulation of germinal center formation / plasma cell differentiation / paraspeckles / germinal center formation / negative regulation of leukocyte proliferation / 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 / erythrocyte development / 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 / 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 / cell morphogenesis / protein localization / 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 / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Robb, G. / Ferguson, A. / Hargreaves, D. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors. Authors: McCoull, W. / Abrams, R.D. / Anderson, E. / Blades, K. / Barton, P. / Box, M. / Burgess, J. / Byth, K. / Cao, Q. / Chuaqui, C. / Carbajo, R.J. / Cheung, T. / Code, E. / Ferguson, A.D. / ...Authors: McCoull, W. / Abrams, R.D. / Anderson, E. / Blades, K. / Barton, P. / Box, M. / Burgess, J. / Byth, K. / Cao, Q. / Chuaqui, C. / Carbajo, R.J. / Cheung, T. / Code, E. / Ferguson, A.D. / Fillery, S. / Fuller, N.O. / Gangl, E. / Gao, N. / Grist, M. / Hargreaves, D. / Howard, M.R. / Hu, J. / Kemmitt, P.D. / Nelson, J.E. / O'Connell, N. / Prince, D.B. / Raubo, P. / Rawlins, P.B. / Robb, G.R. / Shi, J. / Waring, M.J. / Whittaker, D. / Wylot, M. / Zhu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n1z.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n1z.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 5n1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/5n1z ftp://data.pdbj.org/pub/pdb/validation_reports/n1/5n1z | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14215.501 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: Komagataella pastoris (fungus) / References: UniProt: P41182 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-8GQ / |
#4: 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: 2.06 Å3/Da / Density % sol: 40.4 % |
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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: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35.96 Å / Num. obs: 10507 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.34 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.81→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.4 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→13.57 Å / Cor.coef. Fo:Fc: 0.9016 / Cor.coef. Fo:Fc free: 0.8466 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.144
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Displacement parameters | Biso mean: 34.72 Å2
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Refine analyze | Luzzati coordinate error obs: 0.253 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→13.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→2.01 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: -5.6344 Å / Origin y: -1.9492 Å / Origin z: -10.2257 Å
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Refinement TLS group | Selection details: { A|* } |