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- PDB-7okf: Crystal structure of human BCL6 BTB domain in complex with compound 8c -

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Basic information

Entry
Database: PDB / ID: 7okf
TitleCrystal structure of human BCL6 BTB domain in complex with compound 8c
Components
  • ALA-TRP-VAL-ILE-PRO-ALA
  • B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / CANCER / LYMPHOMA / 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 / 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 / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / negative regulation of Notch signaling pathway / 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 / negative regulation of cell growth / chromatin DNA binding / heterochromatin formation / 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
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-VH5 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsCollie, G.W. / Le Bihan, Y.-V. / van Montfort, R.L.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC309/A11566 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2021
Title: Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket.
Authors: Lloyd, M.G. / Huckvale, R. / Cheung, K.J. / Rodrigues, M.J. / Collie, G.W. / Pierrat, O.A. / Gatti Iou, M. / Carter, M. / Davis, O.A. / McAndrew, P.C. / Gunnell, E. / Le Bihan, Y.V. / ...Authors: Lloyd, M.G. / Huckvale, R. / Cheung, K.J. / Rodrigues, M.J. / Collie, G.W. / Pierrat, O.A. / Gatti Iou, M. / Carter, M. / Davis, O.A. / McAndrew, P.C. / Gunnell, E. / Le Bihan, Y.V. / Talbot, R. / Henley, A.T. / Johnson, L.D. / Hayes, A. / Bright, M.D. / Raynaud, F.I. / Meniconi, M. / Burke, R. / van Montfort, R.L.M. / Rossanese, O.W. / Bellenie, B.R. / Hoelder, S.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 2.0Dec 22, 2021Group: Database references / Non-polymer description / Category: chem_comp / citation
Item: _chem_comp.formula / _citation.journal_volume ..._chem_comp.formula / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.1Jan 31, 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: B-cell lymphoma 6 protein
B: ALA-TRP-VAL-ILE-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,26514
Polymers15,1932
Non-polymers1,07312
Water3,675204
1
A: B-cell lymphoma 6 protein
B: ALA-TRP-VAL-ILE-PRO-ALA
hetero molecules

A: B-cell lymphoma 6 protein
B: ALA-TRP-VAL-ILE-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,53128
Polymers30,3854
Non-polymers2,14524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area8510 Å2
ΔGint-62 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.270, 67.270, 165.417
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-490-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 14536.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Plasmid: pET48b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P41182
#2: Protein/peptide ALA-TRP-VAL-ILE-PRO-ALA


Mass: 655.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 216 molecules

#3: Chemical ChemComp-VH5 / 2-chloranyl-4-[[4-(4-methylpiperazin-1-yl)-2-oxidanylidene-1H-quinolin-6-yl]amino]pyridine-3-carbonitrile


Mass: 394.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19ClN6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 2 microliter of the BCL6-BTB/WVIP complex at 4 mg/mL plus 1 microliter of a crystallisation solution consisting of 1 M K2HPO4, 0.7 M NaH2PO4, 75 mM sodium acetate buffer pH 4.5 and 2 % DMSO, ...Details: 2 microliter of the BCL6-BTB/WVIP complex at 4 mg/mL plus 1 microliter of a crystallisation solution consisting of 1 M K2HPO4, 0.7 M NaH2PO4, 75 mM sodium acetate buffer pH 4.5 and 2 % DMSO, against 350 microliter of crystallisation solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.6→33.72 Å / Num. obs: 30154 / % possible obs: 99.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 17.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.025 / Rrim(I) all: 0.102 / Net I/σ(I): 16.5 / Num. measured all: 435154 / Scaling rejects: 455
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
1.6-1.638.91.3961329015000.4090.4961.4831.699.5
8.62-33.7218.20.03745252490.9990.0080.03853.998.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIM

3bim


Resolution: 1.6→33.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.061
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1485 4.94 %RANDOM
Rwork0.167 ---
obs0.167 30075 99.9 %-
Displacement parametersBiso max: 84.13 Å2 / Biso mean: 22.32 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.7414 Å20 Å20 Å2
2---0.7414 Å20 Å2
3---1.4828 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.6→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 66 221 1311
Biso mean--34.36 40.9 -
Num. residues----131
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d438SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes234HARMONIC5
X-RAY DIFFRACTIONt_it1216HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion160SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies27HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1695SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1216HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1653HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion13.49
LS refinement shellResolution: 1.6→1.61 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.23 26 4.32 %
Rwork0.2606 576 -
all0.2593 602 -
obs--99.5 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.86550.8767-2.37571.2608-1.70594.54370.0421-0.02640.06480.0614-0.0298-0.0498-0.13120.2381-0.0123-0.0448-0.0094-0.0106-0.04840.0048-0.0347-28.949327.401612.3952
20.7714-0.59110.56821.7435-0.56882.41130.0674-0.0589-0.03690.15560.10460.2681-0.0019-0.1468-0.1720.0306-0.02110.02320.04610.03830.0346-41.322515.292627.0033
3-0.24040.1307-1.28271.2325-0.63211.11010.0039-0.1154-0.02740.27350.03080.05140.0952-0.235-0.0347-0.0444-0.01810.0182-0.04280.0328-0.071-39.577215.731529.0073
41.25450.81560.11622.061-0.31121.03720.0478-0.019-0.05180.03380.00090.02010.126-0.0342-0.0487-0.0011-0.0178-0.0193-0.04260.0164-0.0081-33.199110.106623.9612
51.83041.8909-2.41262.00330.77870.94460.0419-0.13590.12640.2415-0.2097-0.1055-0.1642-0.13510.16780.0448-0.0466-0.0313-0.01410.0053-0.0006-22.117622.536732.8042
61.56342.00910.19973.93450.9690.69440.1774-0.2776-0.15210.2468-0.1427-0.2230.1580.0628-0.0346-0.0198-0.0276-0.038-0.0460.03710.0013-23.323110.280530.7699
76.90261.48672.1346.82911.58050.2407-0.0710.0315-0.25940.3121-0.0238-0.6234-0.13190.24850.0948-0.0129-0.0305-0.0614-0.01540.05550.0793-13.170914.91531.1356
84.38032.65411.51991.6046-0.500800.0682-0.05440.05620.0204-0.01780.0256-0.0312-0.0087-0.0504-0.0412-0.02870.00090.04440.04070.0073-19.149531.36032.4061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|5 - 27}A5 - 27
2X-RAY DIFFRACTION2{A|28 - 40}A28 - 40
3X-RAY DIFFRACTION3{A|41 - 46}A41 - 46
4X-RAY DIFFRACTION4{A|47 - 92}A47 - 92
5X-RAY DIFFRACTION5{A|93 - 101}A93 - 101
6X-RAY DIFFRACTION6{A|102 - 114}A102 - 114
7X-RAY DIFFRACTION7{A|115 - 129}A115 - 129
8X-RAY DIFFRACTION8{B|0 - 5}B0 - 5

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