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- PDB-1r29: Crystal Structure of the B-Cell Lymphoma 6 (BCL6) BTB Domain to 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r29 | ||||||
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Title | Crystal Structure of the B-Cell Lymphoma 6 (BCL6) BTB Domain to 1.3 Angstrom | ||||||
![]() | B-cell lymphoma 6 protein | ||||||
![]() | TRANSCRIPTION / BTB domain / B-cell lymphoma / transcriptional repression | ||||||
Function / homology | ![]() 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 mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation ...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 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 / 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 Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / 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 immune response / erythrocyte development / heterochromatin formation / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / cell morphogenesis / protein localization / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA 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 / sequence-specific DNA binding / transcription by RNA polymerase II / 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 / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion 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 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427 KB | Display | ![]() |
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Full document | ![]() | 427.8 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.9 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer, generated from the monomer in the asymmetric unit by the operations: (-X,Y,-Z) dx=-1 dy= 0 dz= 0 distance= 2.183 |
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Components
#1: Protein | Mass: 14559.823 Da / Num. of mol.: 1 / Fragment: BTB Domain (Residues 5-129) Mutation: Glycine and serine at N-terminus (cloning artifact), C8Q/C67R/C84N (for solubility) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.86 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: sodium formate, sodium acetate, pH 4.8, 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: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2000 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.3→30 Å / Num. all: 28377 / Num. obs: 27157 / % possible obs: 95.7 % / Redundancy: 3.7 % / Rsym value: 0.051 / Net I/σ(I): 24.4 | |||||||||||||||
Reflection shell | Resolution: 1.3→1.35 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.302 / % possible all: 93.7 | |||||||||||||||
Reflection | *PLUS Highest resolution: 1.3 Å / Rmerge(I) obs: 0.051 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 93.7 % / Rmerge(I) obs: 0.302 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.173 / Rfactor Rwork: 0.1283 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_bond_d / Dev ideal: 0.013 | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.3 Å / Lowest resolution: 1.35 Å |