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- PDB-7oke: Crystal structure of human BCL6 BTB domain in complex with compound 2 -

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Basic information

Entry
Database: PDB / ID: 7oke
TitleCrystal structure of human BCL6 BTB domain in complex with compound 2
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 / 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-VHQ / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 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 1.1Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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

Downloads & links

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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)16,13013
Polymers15,1932
Non-polymers93711
Water3,387188
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)32,25926
Polymers30,3854
Non-polymers1,87422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_575x,x-y+2,-z+1/61
Buried area7670 Å2
ΔGint-46 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.125, 67.125, 164.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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 / Details: Synthetic peptide / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 199 molecules

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


Mass: 310.738 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11ClN4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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

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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.48→47.51 Å / Num. obs: 37651 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.026 / Rrim(I) all: 0.116 / Net I/σ(I): 17.7 / Num. measured all: 718188
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
1.48-1.5318.42.666690036310.5110.6332.7361.3100
5.73-47.5116.80.045134147990.9990.0110.04760.699.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.25data scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIM

3bim


Resolution: 1.48→39.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.059 / SU Rfree Cruickshank DPI: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1791 4.77 %RANDOM
Rwork0.168 ---
obs0.169 37559 100 %-
Displacement parametersBiso max: 98.52 Å2 / Biso mean: 28.34 Å2 / Biso min: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.6275 Å20 Å20 Å2
2---0.6275 Å20 Å2
3---1.255 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.48→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 81 203 1303
Biso mean--43.92 48.03 -
Num. residues----131
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d448SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes264HARMONIC5
X-RAY DIFFRACTIONt_it1261HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion164SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies29HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1765SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1261HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1713HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion13.34
LS refinement shellResolution: 1.48→1.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3555 30 3.99 %
Rwork0.2569 722 -
all0.2607 752 -
obs--99.86 %
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)
13.0270.71312.60260.88691.3134.72210.0613-0.0774-0.08590.0894-0.04040.01330.1657-0.2974-0.0209-0.0177-0.02110.0068-0.0121-0.0109-0.0415-71.597430.760812.5184
20.7252-0.26280.53621.5499-0.361200.0476-0.06830.04580.1450.1422-0.3294-0.05180.1772-0.18980.0869-0.0017-0.02130.0839-0.03630.0686-59.241242.594126.8399
31.08090.00232.18312.02570.25741.4031-0.032-0.11730.02010.31810.0488-0.1263-0.05710.1324-0.0169-0.1083-0.0048-0.0126-0.1255-0.0294-0.1672-61.069342.616828.9676
41.00860.6787-0.22962.12530.49821.34190.0674-0.01050.04960.0104-0.0182-0.0174-0.1652-0.0208-0.04920.01-0.01140.0158-0.0313-0.0191-0.0179-67.3448.27223.8334
52.03981.95341.38392.7309-1.30590.72280.0806-0.2104-0.08960.2904-0.21290.13890.22260.15720.13230.0312-0.04950.03230.0084-0.0084-0.0252-78.564535.822932.8402
61.85292.1339-0.65414.0478-1.40712.73310.1667-0.20310.24980.2378-0.13390.2156-0.1425-0.2014-0.0328-0.0369-0.02140.0392-0.0545-0.0381-0.0267-77.270448.23330.5742
76.72671.3562-1.85228.3339-0.23330.0257-0.1040.1590.21350.1983-0.05640.71870.1037-0.17980.1604-0.0101-0.03310.04640.0273-0.05850.0941-87.376243.619531.1434
84.58531.9831-0.16040.76151.75060.2590.0424-0.0313-0.0127-0.0096-0.03260.10760.13780.0107-0.0097-0.0394-0.0349-0.00490.0483-0.0353-0.0075-81.233626.7412.3602
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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