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- PDB-1r2b: Crystal structure of the BCL6 BTB domain complexed with a SMRT co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r2b | ||||||
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Title | Crystal structure of the BCL6 BTB domain complexed with a SMRT co-repressor peptide | ||||||
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![]() | TRANSCRIPTION / BTB domain / HDAC complex / B-cell lymphoma / transcriptional repression | ||||||
Function / homology | ![]() 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 / regulation of cellular ketone metabolic process ...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 / regulation of cellular ketone metabolic process / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / nuclear glucocorticoid receptor binding / 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 / Notch binding / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / 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 / negative regulation of cellular senescence / Rho protein signal transduction / Regulation of MECP2 expression and activity / estrous cycle / regulation of immune response / erythrocyte development / heterochromatin formation / nuclear retinoid X receptor binding / positive regulation of B cell proliferation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / regulation of cytokine production / : / lactation / transcription repressor complex / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / cell-matrix adhesion / transcription corepressor binding / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / HDACs deacetylate histones / cell motility / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cell morphogenesis / protein localization / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / negative regulation of cell growth / chromatin DNA binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / transcription corepressor activity / sequence-specific double-stranded DNA binding / response to estradiol / 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 / nuclear body / 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 / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ahmad, K.F. / Melnick, A. / Lax, S.A. / Bouchard, D. / Liu, J. / Kiang, C.L. / Mayer, S. / Licht, J.D. / Prive, G.G. | ||||||
![]() | ![]() Title: Mechanism of SMRT corepressor recruitment by the BCL6 BTB domain. Authors: Ahmad, K.F. / Melnick, A. / Lax, S. / Bouchard, D. / Liu, J. / Kiang, C.L. / Mayer, S. / Takahashi, S. / Licht, J.D. / Prive, G.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.4 KB | Display | ![]() |
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PDB format | ![]() | 53.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445 KB | Display | ![]() |
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Full document | ![]() | 451.5 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 14559.823 Da / Num. of mol.: 2 / Fragment: BCL6 (residues 5-129) / Mutation: C8Q, C67R, C84N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2024.325 Da / Num. of mol.: 2 / Fragment: SMRT - BBD (residues 1414-1430) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: PEG 3350, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2001 / Details: Osmic confocal |
Radiation | Monochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 16537 / Num. obs: 16405 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.05 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.256 / % possible all: 92.1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 92.1 % / Rmerge(I) obs: 0.256 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 37.3735 Å2 / ksol: 0.309108 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→27.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.039
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2677 / Rfactor Rwork: 0.2266 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å |