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- PDB-1r2b: Crystal structure of the BCL6 BTB domain complexed with a SMRT co... -

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Basic information

Entry
Database: PDB / ID: 1r2b
TitleCrystal structure of the BCL6 BTB domain complexed with a SMRT co-repressor peptide
Components
  • B-cell lymphoma 6 protein
  • Nuclear receptor co-repressor 2
KeywordsTRANSCRIPTION / BTB domain / HDAC complex / B-cell lymphoma / transcriptional repression
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / 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 ...Loss of MECP2 binding ability to the NCoR/SMRT complex / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / 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 / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / Notch binding / pyramidal neuron differentiation / type 2 immune response / 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 / Notch-HLH transcription pathway / negative regulation of Rho protein signal transduction / erythrocyte development / FOXO-mediated transcription of cell death genes / 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 / estrous cycle / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Rho protein signal transduction / lactation / positive regulation of B cell proliferation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / positive regulation of neuron differentiation / regulation of cytokine production / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / cerebellum development / cell-matrix adhesion / transcription corepressor binding / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / cell motility / negative regulation of cell growth / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / Nuclear Receptor transcription pathway / NOTCH1 Intracellular Domain Regulates Transcription / 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 / nuclear matrix / cell morphogenesis / HCMV Early Events / sequence-specific double-stranded DNA binding / transcription corepressor activity / intracellular protein localization / response to estradiol / heterochromatin formation / regulation of cell population proliferation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / actin cytoskeleton organization / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / nuclear body / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / DNA binding
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / BTB/POZ domain ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Zinc finger, C2H2 type / SANT/Myb domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / Homeobox-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
B-cell lymphoma 6 protein / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAhmad, K.F. / Melnick, A. / Lax, S.A. / Bouchard, D. / Liu, J. / Kiang, C.L. / Mayer, S. / Licht, J.D. / Prive, G.G.
CitationJournal: Mol.Cell / Year: 2003
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
DepositionSep 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
C: Nuclear receptor co-repressor 2
D: Nuclear receptor co-repressor 2


Theoretical massNumber of molelcules
Total (without water)33,1684
Polymers33,1684
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-45 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.228, 38.543, 76.659
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein B-cell lymphoma 6 protein / BCL-6 / Zinc finger protein 51 / LAZ-3 protein / POZ domain / BTB/POZ domain


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.) Homo sapiens (human) / Gene: BCL6 / Plasmid: pET-32(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41182
#2: Protein/peptide Nuclear receptor co-repressor 2 / N-CoR2 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / SMRTe / Thyroid- ...N-CoR2 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / SMRTe / Thyroid- / retinoic-acid-receptor-associated co-repressor / T3 receptor- associating factor / TRAC / CTG repeat protein 26


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.) Homo sapiens (human) / Gene: NCOR2 OR CTG26 / Plasmid: pET-32(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y618
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
225 %PEG33501reservoir
30.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2001 / Details: Osmic confocal
RadiationMonochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→27.08 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 768 -random
Rwork0.227 ---
all0.239 16418 --
obs0.227 15876 96.7 %-
Solvent computationBsol: 37.3735 Å2 / ksol: 0.309108 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.697 Å20 Å2-0.445 Å2
2---5.141 Å20 Å2
3---4.444 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 0 130 2405
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.4831.5
X-RAY DIFFRACTIONc_mcangle_it2.4242
X-RAY DIFFRACTIONc_scbond_it2.1332
X-RAY DIFFRACTIONc_scangle_it3.0872.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.039
RfactorNum. reflection% reflection
Rfree0.399 104 -
Rwork0.298 --
obs-2378 89.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å

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