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- PDB-5mw2: CRYSTAL STRUCTURE OF BCL-6 BTB-domain with BI-3802 -

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Basic information

Entry
Database: PDB / ID: 5mw2
TitleCRYSTAL STRUCTURE OF BCL-6 BTB-domain with BI-3802
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 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 / FOXO-mediated transcription of cell death genes / negative regulation of Rho protein signal transduction / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / 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 / heterochromatin formation / negative regulation of cell growth / chromatin DNA binding / 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
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-U52 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 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 1.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)14,9882
Polymers14,5031
Non-polymers4851
Water25214
1
A: B-cell lymphoma 6 protein
hetero molecules

A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9754
Polymers29,0062
Non-polymers9702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4010 Å2
ΔGint-28 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.367, 72.657, 54.883
Angle α, β, γ (deg.)90.00, 105.87, 90.00
Int Tables number5
Space group name H-MC121

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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 / Source method: isolated from a natural source / Details: BIND CRYSTAL_ID 1008303 / Source: (natural) Homo sapiens (human)
Fragment: Corresponding to pdb id 1R28. Obtained from Emerald BI..
References: UniProt: P41182
#2: Chemical ChemComp-U52 / 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide


Mass: 484.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29ClN6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 22.5 % PEG 3350 2 % isopropanol 0.1 M Calcium cloride 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→52.79 Å / Num. obs: 4788 / % possible obs: 96.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 59.47 Å2 / Net I/σ(I): 10.6
Reflection shellResolution: 2.355→2.365 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION March 1data reduction
autoPROC(Version 1.1.6)data scaling
Aimlessdata scaling
BUSTER2.11.6refinement
RefinementResolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.914 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.736 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.66 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.312
RfactorNum. reflection% reflectionSelection details
Rfree0.283 296 6.18 %RANDOM
Rwork0.247 ---
obs0.249 4786 96.2 %-
Displacement parametersBiso mean: 59.54 Å2
Baniso -1Baniso -2Baniso -3
1-4.077 Å20 Å20.4625 Å2
2--0.6666 Å20 Å2
3----4.7436 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 34 14 1033
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081036HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.911400HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d385SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes25HARMONIC2
X-RAY DIFFRACTIONt_gen_planes147HARMONIC5
X-RAY DIFFRACTIONt_it1036HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.88
X-RAY DIFFRACTIONt_other_torsion18.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion136SEMIHARMONIC5
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_contact1164SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.261 -6.17 %
Rwork0.24 1263 -
all0.242 1346 -
obs--95.12 %
Refinement TLS params.Method: refined / Origin x: 2.1471 Å / Origin y: 19.6019 Å / Origin z: 16.1916 Å
111213212223313233
T-0.074 Å2-0.0441 Å20.0326 Å2--0.0732 Å20.0115 Å2---0.1798 Å2
L1.7955 °20.5412 °21.1901 °2-1.9773 °2-0.0161 °2--4.7031 °2
S-0.052 Å °0.0045 Å °0.0818 Å °-0.1849 Å °0.0492 Å °0.0321 Å °0.0638 Å °-0.1498 Å °0.0028 Å °
Refinement TLS groupSelection details: { A|* }

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