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- PDB-7okm: Crystal structure of human BCL6 BTB domain in complex with compou... -

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Basic information

Entry
Database: PDB / ID: 7okm
TitleCrystal structure of human BCL6 BTB domain in complex with compound 13g
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-VJ2 / 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
AuthorsRodrigues, M.J. / 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)16,12511
Polymers15,1932
Non-polymers9329
Water3,495194
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)32,24922
Polymers30,3854
Non-polymers1,86418
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
MethodPISA
Unit cell
Length a, b, c (Å)68.490, 68.490, 167.476
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 / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 203 molecules

#3: Chemical ChemComp-VJ2 / 2-chloranyl-4-[[1-methyl-2-oxidanylidene-4-(2-pyrimidin-2-ylpropan-2-ylamino)quinolin-6-yl]amino]pyridine-3-carbonitrile / 2-Chloro-4-[[1-methyl-2-oxo-4-(2-pyrimidin-2-ylpropan-2-ylamino)quinolin-6-yl]amino]pyridine-3-carbonitrile / 135385909


Mass: 445.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20ClN7O / 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.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.48→48.4 Å / Num. obs: 39743 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 26.09 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 15.5 / Num. measured all: 485875 / Scaling rejects: 98
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
1.48-1.5111.42.7322200319240.4720.842.8610.999.9
8.11-48.410.40.016347533510.0050.01771.599.6

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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: 1.48→40.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.063 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.057
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1955 4.93 %RANDOM
Rwork0.187 ---
obs0.188 39645 100 %-
Displacement parametersBiso max: 108.74 Å2 / Biso mean: 34.33 Å2 / Biso min: 18.08 Å2
Baniso -1Baniso -2Baniso -3
1--1.675 Å20 Å20 Å2
2---1.675 Å20 Å2
3---3.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.48→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 61 199 1284
Biso mean--38.13 54.32 -
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_planes240HARMONIC5
X-RAY DIFFRACTIONt_it1245HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion160SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies16HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1486SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1245HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg1695HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion12.91
LS refinement shellResolution: 1.48→1.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2631 40 5.04 %
Rwork0.2335 753 -
all0.235 793 -
obs--99.62 %
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)
13.61020.89842.41761.33551.59655.47480.0398-0.0016-0.13560.1242-0.0460.04930.2869-0.44750.0061-0.0755-0.03830.0063-0.0552-0.0217-0.062829.0082-27.977811.8554
22.1448-1.5113-0.82190.8792-0.28170.59490.059-0.0465-0.14730.00790.0636-0.29160.15560.2959-0.12260.03860.0038-0.03330.0993-0.05310.100143.7835-21.744619.5061
3-0.22990.12213.90890.2669-1.10391.3468-0.1277-0.28290.05850.46830.117-0.2403-0.02260.09410.01070.0564-0.0245-0.0323-0.0125-0.0621-0.045740.0361-10.667833.8828
41.30290.15471.03830.34170.19060.96520.0139-0.20560.05910.30740.0625-0.1289-0.06190.1411-0.0764-0.0031-0.004-0.0309-0.0379-0.0396-0.048939.9992-16.109329.3777
53.74462.4802-1.06354.34981.73233.0930.07520.08890.2698-0.29080.104-0.0207-0.48140.0305-0.17920.0555-0.02030.0309-0.03280.00130.021734.2751-7.183918.2359
60.72980.6901-0.30952.94741.3522.42020.1885-0.12560.01810.3737-0.0762-0.1051-0.0229-0.0566-0.11230.0121-0.04450.009-0.0541-0.0198-0.018932.7328-12.972830.1697
72.43611.4759-0.00070.9026-1.47020.42510.0822-0.1579-0.10090.3175-0.21360.11070.10790.14530.13140.0857-0.09260.04260.015-0.0165-0.011322.6886-23.553832.2374
80.64990.60140.61812.78380.24592.51380.2097-0.1450.1940.3559-0.20780.3606-0.1557-0.5014-0.0019-0.073-0.0340.0636-0.0803-0.0469-0.062523.2284-10.635731.3377
96.0835-0.2903-1.71588.4504-0.69060-0.04170.33440.08720.2149-0.17890.39850.1259-0.01980.22060.0087-0.07880.07790.1295-0.11140.103413.7366-14.923831.7178
102.31461.5224-0.16241.0170.25310.0350.0732-0.04040.0351-0.01130.00440.01590.07490.1337-0.0776-0.0885-0.0378-0.01790.0943-0.0802-0.015819.4121-32.79752.102
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 - 33}A28 - 33
3X-RAY DIFFRACTION3{A|34 - 40}A34 - 40
4X-RAY DIFFRACTION4{A|41 - 46}A41 - 46
5X-RAY DIFFRACTION5{A|47 - 68}A47 - 68
6X-RAY DIFFRACTION6{A|69 - 92}A69 - 92
7X-RAY DIFFRACTION7{A|93 - 101}A93 - 101
8X-RAY DIFFRACTION8{A|102 - 114}A102 - 114
9X-RAY DIFFRACTION9{A|115 - 129}A115 - 129
10X-RAY DIFFRACTION10{B|0 - 5}B0 - 5

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