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- PDB-7rv3: Crystal structure of the BCL6 BTB domain in complex with OICR-9124 -

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Basic information

Entry
Database: PDB / ID: 7rv3
TitleCrystal structure of the BCL6 BTB domain in complex with OICR-9124
ComponentsIsoform 2 of B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / immunity / inflammatory response / transcription repressor
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 / regulation of immune system process / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T 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 / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / negative regulation of Notch signaling pathway / B cell proliferation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / 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 / negative regulation of cell growth / chromatin DNA binding / heterochromatin formation / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / protein localization / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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-7R5 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other government Canada
CitationJournal: To Be Published
Title: Structure of the BCL6 BTB domain
Authors: Watson, I. / Isaac, M.
History
DepositionAug 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 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:
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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)15,1765
Polymers14,5601
Non-polymers6164
Water2,000111
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)30,35210
Polymers29,1202
Non-polymers1,2338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4830 Å2
ΔGint-107 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.452, 72.292, 55.154
Angle α, β, γ (deg.)90.000, 105.258, 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-343-

HOH

21A-356-

HOH

31A-361-

HOH

41A-362-

HOH

51A-397-

HOH

61A-406-

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.: 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-7R5 / N-(3-chloropyridin-4-yl)-2-[2-(morpholin-4-yl)-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]acetamide


Mass: 388.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17ClN6O3 / 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-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.: 111 / 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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Co-crystal grown from Ammonium sulfate with Bis-Tris buffer pH 8.8. Shifted to Hepes 7.4 before freezing

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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 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→53.21 Å / Num. obs: 24306 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 11.79 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Rrim(I) all: 0.057 / Net I/σ(I): 14
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3587 / Rpim(I) all: 0.288 / Rrim(I) all: 0.427 / % possible all: 99.2

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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: 1.35→36.15 Å / SU ML: 0.1157 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0318
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186 1203 5.11 %
Rwork0.1589 22326 -
obs0.1604 23529 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.46 Å2
Refinement stepCycle: LAST / Resolution: 1.35→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 38 111 1134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091109
X-RAY DIFFRACTIONf_angle_d1.2121509
X-RAY DIFFRACTIONf_chiral_restr0.0823170
X-RAY DIFFRACTIONf_plane_restr0.0056192
X-RAY DIFFRACTIONf_dihedral_angle_d12.9348426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.410.24081280.21922454X-RAY DIFFRACTION93.93
1.41-1.470.2341290.21192462X-RAY DIFFRACTION93.98
1.47-1.550.22081200.20372443X-RAY DIFFRACTION92.33
1.55-1.650.20781380.17062498X-RAY DIFFRACTION94.41
1.65-1.770.18671440.14612523X-RAY DIFFRACTION95.25
1.77-1.950.17761260.14392482X-RAY DIFFRACTION94.49
1.95-2.240.15941220.12842581X-RAY DIFFRACTION96.88
2.24-2.820.18081460.14732463X-RAY DIFFRACTION93.08
2.82-36.150.18021500.16442420X-RAY DIFFRACTION91.01

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