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- PDB-7rv8: Crystal structure of the BCL6 BTB domain in complex with OICR-10268 -

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Basic information

Entry
Database: PDB / ID: 7rv8
TitleCrystal structure of the BCL6 BTB domain in complex with OICR-10268
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 / 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-7ST / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support1items
OrganizationGrant numberCountry
Other government
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 1.1Apr 3, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2763
Polymers14,5601
Non-polymers7162
Water1,856103
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)30,5526
Polymers29,1202
Non-polymers1,4324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3890 Å2
ΔGint-29 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.768, 72.566, 55.128
Angle α, β, γ (deg.)90.000, 105.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

21A-356-

HOH

31A-382-

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-7ST / N-[5-chloro-2-(morpholin-4-yl)pyridin-4-yl]-2-{5-(3-cyano-4-hydroxy-5-methylphenyl)-3-[3-(1-methyl-1H-pyrazol-4-yl)prop-2-yn-1-yl]-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl}acetamide


Mass: 638.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H28ClN9O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 292 K / Method: microbatch / pH: 4.6
Details: 10% PEG6K with 0.1M MES pH 4.6, 100 mM AmSO4, 10% glycerol, 10% DMSO in Reservoir. Shifted to pH 7.4, 20% glycerol for 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: Aug 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→36.28 Å / Num. obs: 30799 / % possible obs: 96.7 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.022 / Rrim(I) all: 0.041 / Net I/σ(I): 16.6
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
1.25-1.353.40.4452096562130.8590.2830.5292.795.2
3.32-36.283.20.027533416790.9980.0170.03244.295.3

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Processing

Software
NameVersionClassification
Aimless0.3.8data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R_29

Resolution: 1.25→36.28 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.719 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1623 1477 4.8 %RANDOM
Rwork0.1365 ---
obs0.1377 29322 96.53 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 100.21 Å2 / Biso mean: 24.954 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.04 Å2
2--0.04 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.25→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 83 106 1174
Biso mean--31.88 37.6 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191083
X-RAY DIFFRACTIONr_bond_other_d0.0010.021058
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.0091470
X-RAY DIFFRACTIONr_angle_other_deg0.82132412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9755129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05222.85749
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18615195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3631511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
X-RAY DIFFRACTIONr_rigid_bond_restr2.99432138
X-RAY DIFFRACTIONr_sphericity_free27.357544
X-RAY DIFFRACTIONr_sphericity_bonded17.7652179
LS refinement shellResolution: 1.254→1.286 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 121 -
Rwork0.253 2123 -
all-2244 -
obs--94.33 %

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