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Yorodumi- PDB-6zbu: Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with... -
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Basic information
| Entry | Database: PDB / ID: 6zbu | ||||||
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| Title | Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with the NcoR1 BBD1 corepressor peptide | ||||||
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Keywords | TRANSCRIPTION / BCL6 / NCoR1. | ||||||
| Function / homology | Function and homology information: / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / 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 plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes ...: / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / 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 plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / negative regulation of glycolytic process / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / nuclear thyroid hormone receptor binding / pyramidal neuron differentiation / type 2 immune response / negative regulation of JNK cascade / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / positive regulation of cell motility / negative regulation of B cell apoptotic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fatty acid metabolic process / Notch-HLH transcription pathway / negative regulation of Rho protein signal transduction / erythrocyte development / FOXO-mediated transcription of cell death genes / locomotor rhythm / histone deacetylase complex / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of T cell proliferation / B cell proliferation / negative regulation of cellular senescence / Regulation of MECP2 expression and activity / negative regulation of cell-matrix adhesion / negative regulation of Notch signaling pathway / regulation of immune response / Nuclear signaling by ERBB4 / spindle assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Rho protein signal transduction / positive regulation of B cell proliferation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / positive regulation of neuron differentiation / regulation of cytokine production / negative regulation of miRNA transcription / cell-matrix adhesion / nuclear receptor binding / transcription corepressor binding / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cell motility / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / negative regulation of cell growth / Cytoprotection by HMOX1 / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cell morphogenesis / HCMV Early Events / sequence-specific double-stranded DNA binding / mitotic spindle / : / transcription corepressor activity / intracellular protein localization / heterochromatin formation / regulation of cell population proliferation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / actin cytoskeleton organization / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / DNA-binding transcription factor binding / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / inflammatory response / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Zacharchenko, T. / Wright, S.C. | ||||||
| Funding support | United Kingdom, 1items
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Citation | Journal: Iucrj / Year: 2021Title: Functionalization of the BCL6 BTB domain into a noncovalent crystallization chaperone. Authors: Zacharchenko, T. / Wright, S. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6zbu.cif.gz | 453.8 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6zbu.ent.gz | 316.3 KB | Display | PDB format |
| PDBx/mmJSON format | 6zbu.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6zbu_validation.pdf.gz | 549.4 KB | Display | wwPDB validaton report |
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| Full document | 6zbu_full_validation.pdf.gz | 565 KB | Display | |
| Data in XML | 6zbu_validation.xml.gz | 35.1 KB | Display | |
| Data in CIF | 6zbu_validation.cif.gz | 47.9 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/6zbu ftp://data.pdbj.org/pub/pdb/validation_reports/zb/6zbu | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 6xwfC ![]() 6xxsC ![]() 6xyxSC ![]() 6xzzC ![]() 6y17C S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
United Kingdom, 1items
Citation












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