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Yorodumi- PDB-7zwt: Crystal structure of human BCL6 BTB domain in complex with compound 14 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zwt | ||||||
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Title | Crystal structure of human BCL6 BTB domain in complex with compound 14 | ||||||
Components | B-cell lymphoma 6 protein | ||||||
Keywords | TRANSCRIPTION / Inhibitor / Cancer | ||||||
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 / Rho protein signal transduction / regulation of immune response / erythrocyte development / 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 / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||
Authors | Gunnell, E.A. / Le Bihan, Y.-V. / van Montfort, R.L.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays. Authors: Pierrat, O.A. / Liu, M. / Collie, G.W. / Shetty, K. / Rodrigues, M.J. / Le Bihan, Y.V. / Gunnell, E.A. / McAndrew, P.C. / Stubbs, M. / Rowlands, M.G. / Yahya, N. / Shehu, E. / Talbot, R. / ...Authors: Pierrat, O.A. / Liu, M. / Collie, G.W. / Shetty, K. / Rodrigues, M.J. / Le Bihan, Y.V. / Gunnell, E.A. / McAndrew, P.C. / Stubbs, M. / Rowlands, M.G. / Yahya, N. / Shehu, E. / Talbot, R. / Pickard, L. / Bellenie, B.R. / Cheung, K.J. / Drouin, L. / Innocenti, P. / Woodward, H. / Davis, O.A. / Lloyd, M.G. / Varela, A. / Huckvale, R. / Broccatelli, F. / Carter, M. / Galiwango, D. / Hayes, A. / Raynaud, F.I. / Bryant, C. / Whittaker, S. / Rossanese, O.W. / Hoelder, S. / Burke, R. / van Montfort, R.L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zwt.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zwt.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zwt_validation.pdf.gz | 860.8 KB | Display | wwPDB validaton report |
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Full document | 7zwt_full_validation.pdf.gz | 861 KB | Display | |
Data in XML | 7zwt_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 7zwt_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/7zwt ftp://data.pdbj.org/pub/pdb/validation_reports/zw/7zwt | HTTPS FTP |
-Related structure data
Related structure data | 7zwnC 7zwoC 7zwpC 7zwqC 7zwrC 7zwsC 7zwuC 7zwvC 7zwwC 7zwxC 7zwyC 7zwzC 3bimS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16498.953 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 / Plasmid: pET48b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P41182 |
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-Non-polymers , 5 types, 103 molecules
#2: Chemical | ChemComp-K5U / | ||||
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#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 microliter of BCL6-BTB at 10 mg/mL plus 1.5 microliter of a crystallisation solution consisting of 0.1 M Tris pH 7.5 and 0.80 M Na/K Tartrate, against 300 microliter of crystallisation solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.94→55.22 Å / Num. obs: 16240 / % possible obs: 93.2 % / Redundancy: 8.4 % / Biso Wilson estimate: 34.26 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.057 / Rrim(I) all: 0.192 / Net I/σ(I): 6.6 / Num. measured all: 136796 / Scaling rejects: 22 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BIM Resolution: 1.94→17.69 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.844 / SU R Cruickshank DPI: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.134
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Displacement parameters | Biso max: 112.95 Å2 / Biso mean: 40.18 Å2 / Biso min: 18.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→17.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 38
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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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