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- PDB-7rv1: Crystal structure of the BCL6 BTB domain in complex with OICR-8826 -

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Basic information

Entry
Database: PDB / ID: 7rv1
TitleCrystal structure of the BCL6 BTB domain in complex with OICR-8826
ComponentsB-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-7RH / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support1items
OrganizationGrant numberCountry
Ontario Institute for Cancer Research
CitationJournal: To Be Published
Title: Crystal structure of the BCL6 BTB domain in complex with OICR-8826
Authors: Watson, I. / Isaac, M.
History
DepositionAug 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3215
Polymers14,5601
Non-polymers7614
Water2,018112
1
A: B-cell lymphoma 6 protein
hetero molecules

A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,64210
Polymers29,1202
Non-polymers1,5228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4680 Å2
ΔGint-77 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.707, 72.689, 55.478
Angle α, β, γ (deg.)90.000, 106.497, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21A-350-

HOH

31A-362-

HOH

41A-384-

HOH

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Components

#1: Protein 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.: 1 / 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 BL21 (bacteria) / References: UniProt: P41182
#2: Chemical ChemComp-7RH / (E)-3-(7-(2-((3-chloropyridin-4-yl)amino)-2-oxoethyl)-3-(3-(1-methyl-1H-pyrazol-4-yl)prop-2-yn-1-yl)-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)acrylamide


Mass: 490.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19ClN8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 112 / 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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: Ammoniuim sulfate , acetate pH 5.2

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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: Nov 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→36.34 Å / Num. obs: 37804 / % possible obs: 97.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.63 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.05 / Rrim(I) all: 0.082 / Net I/σ(I): 10.9
Reflection shellResolution: 1.17→1.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5171 / Rpim(I) all: 0.36 / Rrim(I) all: 0.566 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122+SVNrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R29

1r29


Resolution: 1.17→30.01 Å / SU ML: 0.0821 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.3703
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1513 1894 5.01 %
Rwork0.129 35905 -
obs0.1301 37799 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 1.17→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 49 112 1137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01391081
X-RAY DIFFRACTIONf_angle_d1.44081470
X-RAY DIFFRACTIONf_chiral_restr0.1024169
X-RAY DIFFRACTIONf_plane_restr0.0122183
X-RAY DIFFRACTIONf_dihedral_angle_d12.6627401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.20.24271420.2112266X-RAY DIFFRACTION87.06
1.2-1.240.18611460.17242505X-RAY DIFFRACTION95.39
1.24-1.270.19251410.14782530X-RAY DIFFRACTION96.36
1.27-1.310.16391390.13892538X-RAY DIFFRACTION97.13
1.31-1.360.17711410.13072551X-RAY DIFFRACTION97.36
1.36-1.420.12391160.11592562X-RAY DIFFRACTION97.38
1.42-1.480.13321350.10352548X-RAY DIFFRACTION98.03
1.48-1.560.13531360.09762614X-RAY DIFFRACTION98.39
1.56-1.660.12961510.09562583X-RAY DIFFRACTION98.7
1.66-1.780.13921060.0982651X-RAY DIFFRACTION98.89
1.78-1.960.11721250.10172614X-RAY DIFFRACTION99.17
1.96-2.250.1481430.10882625X-RAY DIFFRACTION99.6
2.25-2.830.1521450.13152633X-RAY DIFFRACTION99.32
2.83-30.010.1591280.15352685X-RAY DIFFRACTION99.75

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