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Yorodumi- PDB-7rv5: Crystal structure of the BCL6 BTB domain in complex with OICR-9287 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rv5 | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with OICR-9287 | ||||||
Components | Isoform 2 of B-cell lymphoma 6 protein | ||||||
Keywords | TRANSCRIPTION / immunity / inflammatory response / transcription repressor | ||||||
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 / negative regulation of mononuclear cell proliferation ...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 / negative regulation of mononuclear cell proliferation / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / FOXO-mediated transcription of cell death genes / negative regulation of Rho protein signal transduction / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / 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 / heterochromatin formation / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / protein localization / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / Resolution: 2.21 Å | ||||||
Authors | Kuntz, D.A. / Prive, G.G. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Structure of the BCL6 BTB domain Authors: Watson, I. / Isaac, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rv5.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rv5.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rv5_validation.pdf.gz | 792.2 KB | Display | wwPDB validaton report |
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Full document | 7rv5_full_validation.pdf.gz | 793.8 KB | Display | |
Data in XML | 7rv5_validation.xml.gz | 8 KB | Display | |
Data in CIF | 7rv5_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/7rv5 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/7rv5 | HTTPS FTP |
-Related structure data
Related structure data | 7rv3C 7rv4C 7rv6C 7rv7C 7rv8C 7rv9C 1r29S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14559.823 Da / Num. of mol.: 1 / Mutation: C8Q,C67R,C84N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P41182 |
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#2: Chemical | ChemComp-7RB / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.81 % |
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Crystal grow | Temperature: 292 K / Method: microbatch / pH: 6.5 Details: Precipitant solution was 16-20% PEG 8K in 0.1M pH 6.5 Hepes buffer, 50 mM CaCl2 with microseeding. Crystals were soaked in 0.1M Hepes 7.4, 20% PEG 8K, 25% glycerol 0.5 mM ligand prior to ...Details: Precipitant solution was 16-20% PEG 8K in 0.1M pH 6.5 Hepes buffer, 50 mM CaCl2 with microseeding. Crystals were soaked in 0.1M Hepes 7.4, 20% PEG 8K, 25% glycerol 0.5 mM ligand prior to passage through paratone and freezing. Crystals grew as large doubly birefringent rods which were gently crushed. Singly birefringent pieces were selected for data collection. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→52.95 Å / Num. obs: 5769 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.32 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.09 / Rrim(I) all: 0.131 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.21→2.37 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1019 / Rpim(I) all: 0.456 / Rrim(I) all: 0.665 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R29 Resolution: 2.21→36.1 Å / SU ML: 0.2615 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.9824 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.37 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→36.1 Å
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Refine LS restraints |
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LS refinement shell |
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