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- PDB-6y17: Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y17 | ||||||
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Title | Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with nebulinSH3-NCoR1BBD1 | ||||||
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![]() | TRANSCRIPTION / BCL6 / NCoR1. | ||||||
Function / homology | ![]() cardiac muscle thin filament assembly / regulation of actin filament length / somatic muscle development / 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 ...cardiac muscle thin filament assembly / regulation of actin filament length / somatic muscle development / 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 / pyramidal neuron differentiation / negative regulation of JNK cascade / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / T-helper 2 cell differentiation / Striated Muscle Contraction / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of glycolytic process / nuclear thyroid hormone receptor binding / muscle organ development / structural constituent of muscle / 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 / Notch-HLH transcription pathway / 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 / locomotor rhythm / negative regulation of cellular senescence / Rho protein signal transduction / histone deacetylase complex / Regulation of MECP2 expression and activity / regulation of immune response / spindle assembly / erythrocyte development / heterochromatin formation / Nuclear signaling by ERBB4 / positive regulation of B cell proliferation / 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 / HDACs deacetylate histones / cell motility / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / protein localization / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / negative regulation of cell growth / chromatin DNA binding / mitotic spindle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Z disc / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Nuclear Receptor transcription pathway / transcription corepressor activity / sequence-specific double-stranded DNA binding / actin filament binding / Circadian Clock / actin cytoskeleton / chromatin organization / actin 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 / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding 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 | ![]() | 220.3 KB | Display | ![]() |
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PDB format | ![]() | 146.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xwfC ![]() 6xxsC ![]() 6xyxC ![]() 6xzzC ![]() 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: 15602.981 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 8864.005 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: H0Y786, UniProt: O75376, UniProt: P20929*PLUS #3: Chemical | ChemComp-NA / | #4: 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: 2.25 Å3/Da / Density % sol: 45.32 % / Description: Large rods |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.66 M ammonium sulfate, 3.3% (v/v) glycerol, 0.05 M magnesium sulfate, 0.1 M imidazole/ hydrochloric acid pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96884 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→46.88 Å / Num. obs: 58832 / % possible obs: 96.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.31 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.105 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.56→1.6 Å / Rmerge(I) obs: 1.157 / Num. unique obs: 4261 / CC1/2: 0.383 / Rpim(I) all: 0.955 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R28 Resolution: 1.56→34.92 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.8641 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: 27.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→34.92 Å
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Refine LS restraints |
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LS refinement shell |
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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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