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- PDB-7zwy: Crystal structure of human BCL6 BTB domain in complex with compound 21 -

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Basic information

Entry
Database: PDB / ID: 7zwy
TitleCrystal structure of human BCL6 BTB domain in complex with compound 21
Components
  • ALA-TRP-VAL-ILE-PRO-ALA
  • B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / Inhibitor / Cancer
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 mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation ...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 mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation / 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-K6R / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsShetty, K. / Le Bihan, Y.-V. / van Montfort, R.L.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC309/A11566 United Kingdom
CitationJournal: Sci Rep / Year: 2022
Title: Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays.
Authors: Pierrat, O.A. / Liu, M. / Collie, G.W. / Shetty, K. / Rodrigues, M.J. / Le Bihan, Y.V. / Gunnell, E.A. / McAndrew, P.C. / Stubbs, M. / Rowlands, M.G. / Yahya, N. / Shehu, E. / Talbot, R. / ...Authors: Pierrat, O.A. / Liu, M. / Collie, G.W. / Shetty, K. / Rodrigues, M.J. / Le Bihan, Y.V. / Gunnell, E.A. / McAndrew, P.C. / Stubbs, M. / Rowlands, M.G. / Yahya, N. / Shehu, E. / Talbot, R. / Pickard, L. / Bellenie, B.R. / Cheung, K.J. / Drouin, L. / Innocenti, P. / Woodward, H. / Davis, O.A. / Lloyd, M.G. / Varela, A. / Huckvale, R. / Broccatelli, F. / Carter, M. / Galiwango, D. / Hayes, A. / Raynaud, F.I. / Bryant, C. / Whittaker, S. / Rossanese, O.W. / Hoelder, S. / Burke, R. / van Montfort, R.L.M.
History
DepositionMay 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

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)15,5345
Polymers15,1932
Non-polymers3413
Water3,693205
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)31,06810
Polymers30,3854
Non-polymers6826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5970 Å2
ΔGint-68 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.623, 67.623, 164.729
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 , 4 types, 208 molecules

#3: Chemical ChemComp-K6R / 2-chloranyl-4-[(phenylmethyl)amino]pyridine-3-carbonitrile


Mass: 243.692 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10ClN3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→47.73 Å / Num. obs: 27702 / % possible obs: 99.8 % / Redundancy: 34.7 % / Biso Wilson estimate: 23.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.022 / Rrim(I) all: 0.129 / Net I/σ(I): 22.6 / Num. measured all: 960042 / Scaling rejects: 2294
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
1.65-1.6818.92.3512432112900.5270.5392.4181.997.8
9.04-47.7327.40.07665532390.9990.0140.07849.899.5

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3bim


Resolution: 1.65→47.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.075 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.066
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1316 4.76 %RANDOM
Rwork0.163 ---
obs0.164 27625 99.8 %-
Displacement parametersBiso max: 95.11 Å2 / Biso mean: 28.74 Å2 / Biso min: 11.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.4958 Å20 Å20 Å2
2---1.4958 Å20 Å2
3---2.9917 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.65→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 22 215 1246
Biso mean--33.2 47.21 -
Num. residues----131
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d403SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes207HARMONIC5
X-RAY DIFFRACTIONt_it1135HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion156SEMIHARMONIC5
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_contact1531SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1135HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1543HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion13.53
LS refinement shellResolution: 1.65→1.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2828 26 4.7 %
Rwork0.2105 527 -
all0.2133 553 -
obs--95.71 %
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)
12.4041-1.3162-3.15451.72051.53947.1864-0.0613-0.1974-0.0290.0480.0106-0.05360.23680.45060.0507-0.05170.01580.017-0.01470.0119-0.049442.8766-19.3065-14.8039
22.63141.8117-1.8991.7062-0.70331.2190.2533-0.2270.25720.2422-0.04830.1913-0.2762-0.08-0.205-0.00590.00850.04880.01410.006-0.040426.5271-15.39470.6251
33.72610.5174-1.1431.4105-1.34432.04140.01160.1562-0.0363-0.10140.16150.12110.1315-0.2868-0.1731-0.0502-0.0351-0.00930.06390.0516-0.003321.826-24.5396-5.3261
42.6446-0.179-0.53390.6999-1.15053.81380.0505-0.43390.03220.0976-0.0339-0.0021-0.06620.203-0.0165-0.04840.0034-0.00480.07590.0284-0.024737.4111-25.47362.6635
58.24920.10422.04611.4075-0.18173.9905-0.0474-0.4824-0.42830.07760.08930.05720.3208-0.0507-0.0419-0.119-0.00130.0225-0.04660.0746-0.053230.5295-33.15162.9797
68.7627-0.93941.58565.5969-0.7320.18220.0927-0.1006-0.6653-0.0621-0.2540.06390.37540.2770.16130.01430.05760.06110.06810.11770.096839.4348-39.35663.2436
73.9849-3.99-0.13631.8708-1.03140.018-0.06390.0132-0.07030.02210.1057-0.0696-0.09770.055-0.04170.00370.07540.05460.01240.026-0.011351.3087-25.7152-25.0561
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 - 46}A28 - 46
3X-RAY DIFFRACTION3{A|47 - 79}A47 - 79
4X-RAY DIFFRACTION4{A|80 - 101}A80 - 101
5X-RAY DIFFRACTION5{A|102 - 114}A102 - 114
6X-RAY DIFFRACTION6{A|115 - 129}A115 - 129
7X-RAY DIFFRACTION7{B|0 - 5}B0 - 5

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