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- PDB-6cq1: BCL6 BTB domain in complex with 15a -

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Basic information

Entry
Database: PDB / ID: 6cq1
TitleBCL6 BTB domain in complex with 15a
ComponentsB-cell lymphoma 6 protein
Keywordsprotein binding/inhibitor / Protein protein inhibitor / PROTEIN BINDING / protein binding-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 mast cell cytokine production / regulation of germinal center formation / plasma cell differentiation ...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 / plasma cell differentiation / paraspeckles / germinal center formation / negative regulation of leukocyte proliferation / 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 / erythrocyte development / 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 / 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 / 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-F8J / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69921037793 Å
AuthorsLinhares, B.M. / Cheng, H. / Xue, F. / Cierpicki, T.
CitationJournal: J.Med.Chem. / Year: 2018
Title: Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.
Authors: Cheng, H. / Linhares, B.M. / Yu, W. / Cardenas, M.G. / Ai, Y. / Jiang, W. / Winkler, A. / Cohen, S. / Melnick, A. / MacKerell Jr., A. / Cierpicki, T. / Xue, F.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9244
Polymers29,8332
Non-polymers1,0912
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Protein-observed NMR spectroscopy and alpha-lisa assay show compound binding
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-29 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.012, 39.621, 55.225
Angle α, β, γ (deg.)83.654, 73.633, 66.980
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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: 14916.308 Da / Num. of mol.: 2 / Mutation: C10Q; C69R; C86N; E101V
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-F8J / 2-{6-({[2-(1H-indol-3-yl)ethyl]carbamothioyl}amino)-3-[(4-methylpiperazin-1-yl)methyl]-1H-indol-1-yl}-N-(propan-2-yl)acetamide


Mass: 545.742 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H39N7OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: .2 M NaCl, .1 M sodium cacodylate pH 6.0, 8% (w/v) PEG-8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.69→36.47 Å / Num. obs: 22269 / % possible obs: 86.6 % / Redundancy: 2 % / Biso Wilson estimate: 18.0990228994 Å2 / CC1/2: 0.993 / Net I/σ(I): 11.5
Reflection shellResolution: 1.7→1.76 Å / CC1/2: 0.738

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Processing

Software
NameVersionClassification
phenix.refine1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R29
Resolution: 1.69921037793→36.4659139612 Å / SU ML: 0.173549178896 / Cross valid method: FREE R-VALUE / σ(F): 1.98438401923 / Phase error: 27.791401359
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215727137774 1126 5.08443962792 %
Rwork0.180982414365 21020 -
obs0.182696736663 22146 86.5449998046 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.7965450924 Å2
Refinement stepCycle: LAST / Resolution: 1.69921037793→36.4659139612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 78 237 2273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02017711991192111
X-RAY DIFFRACTIONf_angle_d1.432306609522865
X-RAY DIFFRACTIONf_chiral_restr0.0844823316265333
X-RAY DIFFRACTIONf_plane_restr0.00819923071202353
X-RAY DIFFRACTIONf_dihedral_angle_d21.6110493444816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6992-1.77650.2818610870351520.2287014865062850X-RAY DIFFRACTION93.9299123905
1.7765-1.87020.2555990122881670.2091905625742882X-RAY DIFFRACTION95.3408380238
1.8702-1.98740.2467883441681020.1994951144611976X-RAY DIFFRACTION63.9581409665
1.9874-2.14080.2278366457231590.1943605397922873X-RAY DIFFRACTION96.8690095847
2.1408-2.35620.2368382104641420.1971940019022142X-RAY DIFFRACTION70.3418540191
2.3562-2.69710.2392156299011300.1917775667522966X-RAY DIFFRACTION97.7272727273
2.6971-3.39760.2386466123991650.1797766306953007X-RAY DIFFRACTION98.5399192296
3.3976-36.47430.1580614590961090.1543110710892324X-RAY DIFFRACTION76.461345066
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9968587193890.2224036829230.1744972636971.558314328650.4164288253073.04291444896-0.1677508576450.1422571549050.0275660395709-0.3184509038420.153015164314-0.00575268249165-0.3997559011260.258068173186-0.002865303058110.30621309252-0.009869878148910.01137179087550.246361390455-0.01800348776960.121560313674-0.7588668278051.367942714141.46817855233
20.5535126657060.0745609066710.300856486331.07732020021-0.1363186147222.91526376886-0.160515286761-0.1580070817680.05029361389340.2695148150650.1363566502860.0346379369112-0.436833833599-0.282854218940.03707679403470.3375608683210.1513666328460.0199856625870.269042590177-0.03081063906520.148218158164-12.03837012661.4178803554121.9735931623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 6:128)
2X-RAY DIFFRACTION2(chain B and resseq 6:128)

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