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- PDB-6xyx: Crystal structure of the BCL6 BTB domain in complex with the NCoR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xyx | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD corepressor peptide | ||||||
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![]() | TRANSCRIPTION / BCL6 / NCoR1. | ||||||
Function / homology | ![]() NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / 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 androgen receptor signaling pathway ...NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / 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 androgen receptor signaling pathway / 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 / negative regulation of JNK cascade / 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 / negative regulation of glycolytic process / nuclear thyroid hormone receptor binding / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / negative regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / regulation of T cell proliferation / negative regulation of Notch signaling pathway / regulation of cell differentiation / Notch-HLH transcription pathway / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / locomotor rhythm / negative regulation of cellular senescence / histone deacetylase complex / Rho protein signal transduction / Regulation of MECP2 expression and activity / regulation of immune response / spindle assembly / erythrocyte development / positive regulation of B cell proliferation / Nuclear signaling by ERBB4 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / regulation of cytokine production / transcription repressor complex / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cell-matrix adhesion / transcription corepressor binding / negative regulation of miRNA transcription / nuclear receptor binding / cell motility / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / heterochromatin formation / PPARA activates gene expression / Cytoprotection by HMOX1 / negative regulation of cell growth / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / sequence-specific double-stranded DNA binding / protein localization / Circadian Clock / chromatin organization / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / 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 / chromatin Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zacharchenko, T. / Wright, S.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Functionalization of the BCL6 BTB domain into a noncovalent crystallization chaperone. Authors: Zacharchenko, T. / Wright, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.4 KB | Display | ![]() |
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PDB format | ![]() | 102 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6xwfC ![]() 6xxsC ![]() 6xzzC ![]() 6y17C ![]() 6zbuC ![]() 1r28S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14498.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1942.288 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium acetate trihydrate 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→68.88 Å / Num. obs: 56791 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.44→1.52 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8133 / CC1/2: 0.606 / Rpim(I) all: 0.894 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R28 Resolution: 1.44→21.63 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.05 Å2 / Biso mean: 31.6561 Å2 / Biso min: 16.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.44→21.63 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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