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- PDB-6xzz: 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: 6xzz | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD2 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 / 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 / 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 / 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 / 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 / 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 | ![]() | 87.3 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.6 KB | Display | ![]() |
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Full document | ![]() | 446.2 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xwfC ![]() 6xxsC ![]() 6xyxC ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 14498.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1865.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 131 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TFA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TFA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NA / #4: Chemical | #5: Chemical | ChemComp-TFA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 13.4%(v/v) PEG 400, 0.335M K2HPO4 / NaH2PO4 pH 7.5 |
-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: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→54.22 Å / Num. obs: 41626 / % possible obs: 100 % / Redundancy: 18.3 % / Biso Wilson estimate: 14.57 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.39→1.41 Å / Num. unique obs: 2036 / CC1/2: 0.524 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R28 Resolution: 1.39→54.22 Å / SU ML: 0.1804 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.039 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: 21.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→54.22 Å
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Refine LS restraints |
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LS refinement shell |
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