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- PDB-7ruy: Crystal structure of the BCL6 BTB domain in complex with OICR-8388 -

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Basic information

Entry
Database: PDB / ID: 7ruy
TitleCrystal structure of the BCL6 BTB domain in complex with OICR-8388
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 mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation ...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 mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation / plasma cell differentiation / paraspeckles / germinal center formation / pyramidal neuron differentiation / type 2 immune response / regulation of immune system process / 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 / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / 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 / DNA-binding transcription factor binding / Interleukin-4 and Interleukin-13 signaling / 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-7S0 / FORMIC ACID / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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-8388
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)15,2136
Polymers14,5601
Non-polymers6535
Water1,76598
1
A: B-cell lymphoma 6 protein
hetero molecules

A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,42612
Polymers29,1202
Non-polymers1,30610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5310 Å2
ΔGint-28 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.447, 72.180, 55.538
Angle α, β, γ (deg.)90.000, 107.128, 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-347-

HOH

21A-358-

HOH

31A-374-

HOH

41A-396-

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 (E. coli) / References: UniProt: P41182
#2: Chemical ChemComp-7S0 / N-(3-chloropyridin-4-yl)-2-(2-{[(2,4-dimethoxyphenyl)methyl]amino}-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)acetamide


Mass: 468.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21ClN6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: sodium formate, sodium acetate, pH 4.8

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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: Jun 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→27.25 Å / Num. obs: 28364 / % possible obs: 93.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 12.73 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.033 / Rrim(I) all: 0.053 / Net I/σ(I): 16
Reflection shellResolution: 1.27→1.34 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3 / Num. unique obs: 4075 / CC1/2: 0.78 / Rpim(I) all: 0.32 / Rrim(I) all: 0.513 / % possible all: 92.7

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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
Resolution: 1.27→27.25 Å / SU ML: 0.1166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1711 1402 5.02 %
Rwork0.1433 26511 -
obs0.1448 27913 91.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.76 Å2
Refinement stepCycle: LAST / Resolution: 1.27→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 45 98 1128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01171101
X-RAY DIFFRACTIONf_angle_d1.2871494
X-RAY DIFFRACTIONf_chiral_restr0.0791171
X-RAY DIFFRACTIONf_plane_restr0.0097191
X-RAY DIFFRACTIONf_dihedral_angle_d18.0381423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.310.23171210.21752597X-RAY DIFFRACTION89.82
1.31-1.370.26261400.18872613X-RAY DIFFRACTION91.98
1.37-1.430.22981330.18132583X-RAY DIFFRACTION89.49
1.43-1.50.23431290.152534X-RAY DIFFRACTION87.31
1.5-1.60.14861330.12282675X-RAY DIFFRACTION93.13
1.6-1.720.14541460.12692676X-RAY DIFFRACTION92.46
1.72-1.890.19191480.12072606X-RAY DIFFRACTION90.86
1.89-2.170.14611510.11052805X-RAY DIFFRACTION96.73
2.17-2.730.141330.13732667X-RAY DIFFRACTION92.59
2.73-27.250.17471680.1552755X-RAY DIFFRACTION94.38

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