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- PDB-7bde: HUMAN BCL6 BTB-DOMAIN IN COMPLEX WITH GSK137 -

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Basic information

Entry
Database: PDB / ID: 7bde
TitleHUMAN BCL6 BTB-DOMAIN IN COMPLEX WITH GSK137
ComponentsIsoform 2 of B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / BTB DOMAIN / B-CELL LYMPHOMA / TRANSCRIPTIONAL REPRESSION TRANSCRIPTION / 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 / 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
BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Chem-TEQ / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.044 Å
AuthorsSomers, D.O.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: GSK137, a potent small-molecule BCL6 inhibitor with in vivo activity, suppresses antibody responses in mice.
Authors: Pearce, A.C. / Bamford, M.J. / Barber, R. / Bridges, A. / Convery, M.A. / Demetriou, C. / Evans, S. / Gobbetti, T. / Hirst, D.J. / Holmes, D.S. / Hutchinson, J.P. / Jayne, S. / Lezina, L. / ...Authors: Pearce, A.C. / Bamford, M.J. / Barber, R. / Bridges, A. / Convery, M.A. / Demetriou, C. / Evans, S. / Gobbetti, T. / Hirst, D.J. / Holmes, D.S. / Hutchinson, J.P. / Jayne, S. / Lezina, L. / McCabe, M.T. / Messenger, C. / Morley, J. / Musso, M.C. / Scott-Stevens, P. / Manso, A.S. / Schofield, J. / Slocombe, T. / Somers, D. / Walker, A.L. / Wyce, A. / Zhang, X.P. / Wagner, S.D.
History
DepositionDec 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1014
Polymers15,5571
Non-polymers5453
Water1,69394
1
A: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules

A: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2038
Polymers31,1142
Non-polymers1,0896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area5240 Å2
ΔGint-21 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.251, 49.251, 124.409
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

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Components

#1: Protein Isoform 2 of B-cell lymphoma 6 protein / BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing ...BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing protein 27 / Zinc finger protein 51


Mass: 15556.799 Da / Num. of mol.: 1 / Fragment: BTB DOMAIN (RESIDUES 5-129) / Mutation: YES
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: Chemical ChemComp-TEQ / 5-[(5S,7R)-3-fluoranyl-7-(2-methylpyridin-3-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidin-5-yl]quinolin-2-amine / 5-[(5~{S},7~{R})-3-fluoranyl-7-(2-methylpyridin-3-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidin-5-yl]quinolin-2-amine


Mass: 374.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19FN6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Glycerol, BisTris Propane / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 23, 2019
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.044→40.347 Å / Num. obs: 7572 / % possible obs: 64.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.167 / Rsym value: 0.167 / Net I/σ(I): 11
Reflection shellResolution: 2.044→2.249 Å / Redundancy: 10 % / Rmerge(I) obs: 2.195 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 379 / CC1/2: 0.784 / Rpim(I) all: 0.717 / Rrim(I) all: 2.314 / Rsym value: 2.195 / % possible all: 13.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSVERSION Mar 15, 2019 BUILT=20190806data processing
Aimless0.7.4data reduction
STARANISO2.2.19data scaling
REFMAC5.8.0253refinement
REFMAC5.8.0253phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: IN-HOUSE DERIVED

Resolution: 2.044→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.879 / SU ML: 0.191 / SU R Cruickshank DPI: 0.2939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 377 5.1 %RANDOM
Rwork0.1802 ---
obs0.1834 7062 63.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 136.62 Å2 / Biso mean: 47.056 Å2 / Biso min: 26.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2.044→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 38 94 1140
Biso mean--55.07 50.88 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171006
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.6231433
X-RAY DIFFRACTIONr_angle_other_deg1.1911.5962313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69621.01759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65315190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3911510
X-RAY DIFFRACTIONr_chiral_restr0.060.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
LS refinement shellResolution: 2.044→2.096 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 4 -
Rwork0.408 28 -
all-32 -
obs--3.87 %

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