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Yorodumi- PDB-4cp3: The structure of BCL6 BTB (POZ) domain in complex with the ansamy... -
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-Basic information
Entry | Database: PDB / ID: 4cp3 | ||||||
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Title | The structure of BCL6 BTB (POZ) domain in complex with the ansamycin antibiotic rifabutin. | ||||||
Components | B-CELL LYMPHOMA 6 PROTEIN | ||||||
Keywords | IMMUNE SYSTEM / BTB/POZ / TRANSCRIPTIONAL REPRESSOR / RIFAMYCIN / ANTIBIOTIC / SMRT / INHIBITOR | ||||||
Function / homology | Function and homology information 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 / plasma cell differentiation ...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 / plasma cell differentiation / paraspeckles / germinal center formation / negative regulation of leukocyte proliferation / 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 / erythrocyte development / 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 / 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 / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Evans, S.E. / Fairall, L. / Goult, B.T. / Jamieson, A.G. / Ferrigno, P.K. / Ford, R. / Wagner, S.D. / Schwabe, J.W.R. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: The Ansamycin Antibiotic, Rifamycin Sv, Inhibits Bcl6 Transcriptional Repression and Forms a Complex with the Bcl6-Btb/Poz Domain. Authors: Evans, S.E. / Goult, B.T. / Fairall, L. / Jamieson, A.G. / Ko Ferrigno, P. / Ford, R. / Schwabe, J.W.R. / Wagner, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cp3.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cp3.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 4cp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/4cp3 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cp3 | HTTPS FTP |
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-Related structure data
Related structure data | 1r2bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14228.543 Da / Num. of mol.: 2 / Fragment: BTB DOMAIN, RESIDUES 9-128 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P41182 #2: Chemical | ChemComp-RBT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.17 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 20% PEG 6000, 100MM SODIUM CITRATE, PH 5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.82 Å / Num. obs: 9168 / % possible obs: 97 % / Observed criterion σ(I): 4.1 / Redundancy: 3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 4.1 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R2B Resolution: 2.3→57.92 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.878 / SU B: 9.861 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.688 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.366 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→57.92 Å
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