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- PDB-7rv3: Crystal structure of the BCL6 BTB domain in complex with OICR-9124 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rv3 | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with OICR-9124 | ||||||
![]() | Isoform 2 of B-cell lymphoma 6 protein | ||||||
![]() | TRANSCRIPTION / immunity / inflammatory response / transcription repressor | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuntz, D.A. / Prive, G.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the BCL6 BTB domain Authors: Watson, I. / Isaac, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.8 KB | Display | ![]() |
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PDB format | ![]() | 72.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735.7 KB | Display | ![]() |
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Full document | ![]() | 736.1 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rv4C ![]() 7rv5C ![]() 7rv6C ![]() 7rv7C ![]() 7rv8C ![]() 7rv9C ![]() 1r29S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-7R5 / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Co-crystal grown from Ammonium sulfate with Bis-Tris buffer pH 8.8. Shifted to Hepes 7.4 before freezing |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→53.21 Å / Num. obs: 24306 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 11.79 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Rrim(I) all: 0.057 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3587 / Rpim(I) all: 0.288 / Rrim(I) all: 0.427 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R29 Resolution: 1.35→36.15 Å / SU ML: 0.1157 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0318 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: 17.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→36.15 Å
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Refine LS restraints |
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LS refinement shell |
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