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Yorodumi- PDB-3bim: Crystal structure of the BCL6 BTB domain dimer in complex with th... -
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-Basic information
Entry | Database: PDB / ID: 3bim | ||||||
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Title | Crystal structure of the BCL6 BTB domain dimer in complex with the BCOR BBD corepressor peptide | ||||||
Components |
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Keywords | TRANSCRIPTION REPRESSOR / protein-peptide compex / Activator / Chromosomal rearrangement / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Proto-oncogene / Repressor / Transcription / Transcription regulation / Zinc / Zinc-finger / Alternative splicing / ANK repeat / Chromatin regulator / Disease mutation | ||||||
Function / homology | Function and homology information negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / blastocyst hatching / 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 ...negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / blastocyst hatching / 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 bone mineralization / 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 / regulation of immune system process / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / odontogenesis / 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 / roof of mouth development / negative regulation of Notch signaling pathway / regulation of cell differentiation / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / positive regulation of B cell proliferation / regulation of cytokine production / heat shock protein binding / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell morphogenesis / heterochromatin formation / negative regulation of cell growth / chromatin DNA binding / histone deacetylase binding / transcription corepressor activity / sequence-specific double-stranded DNA binding / protein localization / regulation of inflammatory response / heart development / regulation of cell population proliferation / actin cytoskeleton organization / DNA-binding transcription factor binding / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / transcription cis-regulatory region binding / transcription by RNA polymerase II / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / chromatin binding / DNA damage response / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Prive, G.G. / Ghetu, A.F. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer. Authors: Ghetu, A.F. / Corcoran, C.M. / Cerchietti, L. / Bardwell, V.J. / Melnick, A. / Prive, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bim.cif.gz | 229.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bim.ent.gz | 187.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bim_validation.pdf.gz | 563.1 KB | Display | wwPDB validaton report |
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Full document | 3bim_full_validation.pdf.gz | 601.7 KB | Display | |
Data in XML | 3bim_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 3bim_validation.cif.gz | 61.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/3bim ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3bim | HTTPS FTP |
-Related structure data
Related structure data | 1r29S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14559.823 Da / Num. of mol.: 8 / Fragment: BTB domain (also known as the POZ domain) / Mutation: C8Q, C67R, C84N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P41182 #2: Protein/peptide | Mass: 1928.128 Da / Num. of mol.: 8 / Fragment: BBD (BTB binding domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCOR / Production host: Escherichia coli (E. coli) / References: UniProt: Q6W2J9 #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: 3.87 Å3/Da / Density % sol: 68.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 75 mM NaAcetate, 900 mM K2HPO4, 700 NaH2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.7 Å / Num. all: 65050 / Num. obs: 63099 / % possible obs: 97 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 5.3 / % possible all: 98.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R29 Resolution: 2.6→48.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.457 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.364 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 71.704 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→48.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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