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- PDB-7t0t: Crystal structure of the BCL6 BTB domain in complex with OICR-10562 -

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Basic information

Entry
Database: PDB / ID: 7t0t
TitleCrystal structure of the BCL6 BTB domain in complex with OICR-10562
ComponentsIsoform 2 of B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / immunity / inflammatory response / transcription repressor / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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-E1I / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Ontario Institute for Cancer Research Canada
CitationJournal: To Be Published
Title: Crystal structure of the BCL6 BTB domain in complex with OICR-10562
Authors: Kuntz, D.A. / Prive, G.G.
History
DepositionNov 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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
B: Isoform 2 of B-cell lymphoma 6 protein
C: Isoform 2 of B-cell lymphoma 6 protein
D: Isoform 2 of B-cell lymphoma 6 protein
E: Isoform 2 of B-cell lymphoma 6 protein
F: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,20014
Polymers87,3596
Non-polymers3,8418
Water6,630368
1
A: Isoform 2 of B-cell lymphoma 6 protein
B: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4265
Polymers29,1202
Non-polymers1,3063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-31 kcal/mol
Surface area13110 Å2
MethodPISA
2
C: Isoform 2 of B-cell lymphoma 6 protein
D: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3484
Polymers29,1202
Non-polymers1,2282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-31 kcal/mol
Surface area12970 Å2
MethodPISA
3
E: Isoform 2 of B-cell lymphoma 6 protein
F: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4265
Polymers29,1202
Non-polymers1,3063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-29 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.592, 102.549, 65.028
Angle α, β, γ (deg.)90.000, 115.480, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 14559.823 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41182
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-E1I / N-[5-chloro-2-(morpholin-4-yl)pyridin-4-yl]-2-[5-(3-cyano-4-hydroxy-5-methylphenyl)-3-methyl-2-(1-methyl-1H-pyrazol-4-yl)-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]acetamide


Mass: 614.054 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C30H28ClN9O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.8
Details: 2.25M NaCl precipitant pH 4.8 Acetate as buffer with 10% glycerol, 10% DMSO and 0.2M LiSO4 in microbatch.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50.95 Å / Num. obs: 49900 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.08 / Rrim(I) all: 0.171 / Net I/σ(I): 8.9 / Num. measured all: 224733
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.110.8063258072630.6010.4330.9182.699.9
6.33-50.950.066720716080.9960.0340.07521.898.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R29

1r29


Resolution: 2→32.36 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 2544 5.1 %
Rwork0.1807 47301 -
obs0.1827 49845 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.95 Å2
Refinement stepCycle: LAST / Resolution: 2→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5860 0 272 368 6500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666452
X-RAY DIFFRACTIONf_angle_d0.79278783
X-RAY DIFFRACTIONf_dihedral_angle_d18.90222409
X-RAY DIFFRACTIONf_chiral_restr0.0472993
X-RAY DIFFRACTIONf_plane_restr0.00781100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.28721510.24692610X-RAY DIFFRACTION99.82
2.04-2.080.28951240.23642633X-RAY DIFFRACTION99.82
2.08-2.130.26041330.22522623X-RAY DIFFRACTION99.86
2.13-2.180.21661030.21432660X-RAY DIFFRACTION99.78
2.18-2.230.27341140.21052654X-RAY DIFFRACTION99.78
2.23-2.290.26031660.22432563X-RAY DIFFRACTION99.42
2.29-2.360.24121310.19282647X-RAY DIFFRACTION99.86
2.36-2.430.2471570.18742611X-RAY DIFFRACTION99.89
2.43-2.520.21741470.19112641X-RAY DIFFRACTION99.96
2.52-2.620.24851360.18352628X-RAY DIFFRACTION99.93
2.62-2.740.24311040.18252655X-RAY DIFFRACTION99.86
2.74-2.880.22441190.1862655X-RAY DIFFRACTION99.86
2.88-3.070.22971710.17842600X-RAY DIFFRACTION99.86
3.07-3.30.21091510.16982620X-RAY DIFFRACTION99.75
3.3-3.630.19781430.16052635X-RAY DIFFRACTION99.71
3.63-4.160.15621410.14782636X-RAY DIFFRACTION99.46
4.16-5.240.1852030.14022586X-RAY DIFFRACTION99.39
5.24-32.360.25561500.19892644X-RAY DIFFRACTION98.62

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