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- PDB-5mwd: Crystal structure of the BCL6 BTB-domain with compound 2 -

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Basic information

Entry
Database: PDB / ID: 5mwd
TitleCrystal structure of the BCL6 BTB-domain with compound 2
ComponentsB-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / Inhibitor
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 / 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 / erythrocyte development / Rho protein signal transduction / regulation of immune response / 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 / protein localization / cell morphogenesis / 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 / metal ion binding / nucleus
Similarity search - Function
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TJ3 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsBader, G. / Flotzinger, G. / Weiss-Puxbaum, A. / Zoephel, A.
CitationJournal: Cell Rep / Year: 2017
Title: Chemically Induced Degradation of the Oncogenic Transcription Factor BCL6.
Authors: Kerres, N. / Steurer, S. / Schlager, S. / Bader, G. / Berger, H. / Caligiuri, M. / Dank, C. / Engen, J.R. / Ettmayer, P. / Fischerauer, B. / Flotzinger, G. / Gerlach, D. / Gerstberger, T. / ...Authors: Kerres, N. / Steurer, S. / Schlager, S. / Bader, G. / Berger, H. / Caligiuri, M. / Dank, C. / Engen, J.R. / Ettmayer, P. / Fischerauer, B. / Flotzinger, G. / Gerlach, D. / Gerstberger, T. / Gmaschitz, T. / Greb, P. / Han, B. / Heyes, E. / Iacob, R.E. / Kessler, D. / Kolle, H. / Lamarre, L. / Lancia, D.R. / Lucas, S. / Mayer, M. / Mayr, K. / Mischerikow, N. / Muck, K. / Peinsipp, C. / Petermann, O. / Reiser, U. / Rudolph, D. / Rumpel, K. / Salomon, C. / Scharn, D. / Schnitzer, R. / Schrenk, A. / Schweifer, N. / Thompson, D. / Traxler, E. / Varecka, R. / Voss, T. / Weiss-Puxbaum, A. / Winkler, S. / Zheng, X. / Zoephel, A. / Kraut, N. / McConnell, D. / Pearson, M. / Koegl, M.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,8582
Polymers14,5031
Non-polymers3551
Water1,71195
1
A: B-cell lymphoma 6 protein
hetero molecules

A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7154
Polymers29,0062
Non-polymers7102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3900 Å2
ΔGint-30 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.311, 71.761, 54.873
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

21A-350-

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: 14502.771 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-TJ3 / 5-[[5-chloranyl-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-yl]amino]-1,3-dihydroindol-2-one


Mass: 354.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15ClN6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 25 % PEG 3350 15 % Isopropanol 0.2 M Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→35.88 Å / Num. obs: 9606 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.02 Å2 / Net I/σ(I): 12.6

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
RefinementResolution: 1.85→35.88 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.149 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.132
RfactorNum. reflection% reflectionSelection details
Rfree0.209 488 5.11 %RANDOM
Rwork0.167 ---
obs0.169 9552 98.7 %-
Displacement parametersBiso mean: 29.26 Å2
Baniso -1Baniso -2Baniso -3
1--8.2235 Å20 Å2-8.0008 Å2
2--6.9282 Å20 Å2
3---1.2953 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.85→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 25 95 1095
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081027HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.941388HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d370SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes25HARMONIC2
X-RAY DIFFRACTIONt_gen_planes148HARMONIC5
X-RAY DIFFRACTIONt_it1027HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion15.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion134SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1266SEMIHARMONIC4
LS refinement shellResolution: 1.85→2.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.217 134 4.96 %
Rwork0.196 2565 -
all0.197 2699 -
obs--98.9 %
Refinement TLS params.Method: refined / Origin x: 1.8917 Å / Origin y: 18.9181 Å / Origin z: 15.9726 Å
111213212223313233
T-0.0014 Å2-0.0296 Å2-0.0024 Å2--0.0392 Å20.0015 Å2---0.0499 Å2
L0.6945 °20.0281 °2-0.1137 °2-0.5977 °2-0.1947 °2--1.2102 °2
S-0.05 Å °0.1074 Å °0.0238 Å °-0.1068 Å °0.0121 Å °-0.0296 Å °0.117 Å °-0.1156 Å °0.0379 Å °
Refinement TLS groupSelection details: { A|* }

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