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- PDB-7t0s: Crystal structure of the BCL6 BTB domain in complex with OICR-11864 -

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Basic information

Entry
Database: PDB / ID: 7t0s
TitleCrystal structure of the BCL6 BTB domain in complex with OICR-11864
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-E2E / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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-11864
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6199
Polymers43,6793
Non-polymers1,9406
Water3,207178
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)30,5228
Polymers29,1202
Non-polymers1,4026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5060 Å2
ΔGint-39 kcal/mol
Surface area12070 Å2
MethodPISA
2
B: Isoform 2 of B-cell lymphoma 6 protein
C: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3595
Polymers29,1202
Non-polymers1,2393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-28 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.740, 72.290, 55.330
Angle α, β, γ (deg.)90.000, 108.320, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21A-332-

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: 14559.823 Da / Num. of mol.: 3
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-E2E / 3-chloro-5-{1-[2-({5-chloro-2-[(3S)-3-methylmorpholin-4-yl]pyridin-4-yl}amino)-2-oxoethyl]-4-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl}-2-hydroxybenzamide


Mass: 573.403 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H23Cl2FN6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 21% PEG6K as precipitant in pH 6.6 Cacodylate 10% DMSO +100 mM AmSO4 Crystal cryoprotected in resevoir buffer containing 25% glycerol

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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: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.856→55.869 Å / Num. obs: 29330 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 26.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.041 / Rrim(I) all: 0.088 / Net I/σ(I): 10.6 / Num. measured all: 131396
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.856-1.8624.20.70911732800.8660.3920.8132.396.6
8.605-55.8694.10.03312893130.9990.0180.03720.698.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R29

1r29


Resolution: 1.86→29.78 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1377 4.71 %
Rwork0.2117 27854 -
obs0.2134 29231 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.42 Å2 / Biso mean: 34.8802 Å2 / Biso min: 14.86 Å2
Refinement stepCycle: final / Resolution: 1.86→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 277 187 3382
Biso mean--32.15 41.67 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073184
X-RAY DIFFRACTIONf_angle_d1.0544327
X-RAY DIFFRACTIONf_dihedral_angle_d16.0411166
X-RAY DIFFRACTIONf_chiral_restr0.065496
X-RAY DIFFRACTIONf_plane_restr0.011533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.920.33411290.30162747287699
1.92-20.2941480.267128062954100
2-2.090.24741250.23742755288099
2.09-2.20.25241230.222727972920100
2.2-2.340.23291420.203727822924100
2.34-2.520.23991420.20192767290999
2.52-2.770.24321530.207527772930100
2.77-3.170.24311390.20227882927100
3.17-3.990.21511300.185628102940100
4-29.780.27011460.21582825297199

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