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Yorodumi- PDB-7rv6: Crystal structure of the BCL6 BTB domain in complex with OICR-9288 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rv6 | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with OICR-9288 | ||||||
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 / 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 / Resolution: 1.683 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 | 7rv6.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rv6.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rv6_validation.pdf.gz | 803.3 KB | Display | wwPDB validaton report |
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Full document | 7rv6_full_validation.pdf.gz | 804 KB | Display | |
Data in XML | 7rv6_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 7rv6_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/7rv6 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/7rv6 | HTTPS FTP |
-Related structure data
Related structure data | 7rv3C 7rv4C 7rv5C 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-7SC / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 1.98 Å3/Da / Density % sol: 37.83 % |
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Crystal grow | Temperature: 292 K / Method: microbatch / pH: 7.4 Details: 16-20% PEG 8K in 0.1M pH 7.4 Hepes buffer, 50 mM CaCl2. 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. |
-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: Jun 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.683→36.11 Å / Num. obs: 12370 / % possible obs: 96 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.87 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.68→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 132 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R29 Resolution: 1.683→36.11 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.491 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.683→36.11 Å
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