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- PDB-7rv7: Crystal structure of the BCL6 BTB domain in complex with OICR-9322 -

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Basic information

Entry
Database: PDB / ID: 7rv7
TitleCrystal structure of the BCL6 BTB domain in complex with OICR-9322
ComponentsIsoform 2 of B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / immunity / inflammatory response / transcription repressor
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-7SH / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other government Canada
CitationJournal: To Be Published
Title: Structure of the BCL6 BTB domain
Authors: Watson, I. / Isaac, M.
History
DepositionAug 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3235
Polymers14,5601
Non-polymers7634
Water1,47782
1
A: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules

A: Isoform 2 of B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,64610
Polymers29,1202
Non-polymers1,5268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5280 Å2
ΔGint-31 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.556, 74.943, 53.083
Angle α, β, γ (deg.)90.000, 104.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-204-

CA

21A-331-

HOH

31A-353-

HOH

41A-379-

HOH

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Components

#1: Protein Isoform 2 of 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: 14559.823 Da / Num. of mol.: 1 / Mutation: C8Q,C67R,C84N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P41182
#2: Chemical ChemComp-7SH / N-(3-chloropyridin-4-yl)-2-{5-(3-cyano-4-hydroxyphenyl)-3-[3-(1-methyl-1H-pyrazol-4-yl)prop-2-yn-1-yl]-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl}acetamide


Mass: 538.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H19ClN8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 292 K / Method: microbatch / pH: 6
Details: Precipitant solution was 16-20% PEG 8K in 0.1M pH 6. BisTris buffer. Crystals were soaked in 0.1M Hepes 7.4, 20% PEG 8K, 25% glycerol 0.5 mM ligand prior to passage through paratone and freezing.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→37.47 Å / Num. obs: 14298 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Net I/σ(I): 14.4 / Num. measured all: 46448
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
1.63-1.823.30.3471345940380.910.2220.4133.398.8
3.64-37.473.20.025422213080.9980.0160.02939.698.5

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→30.26 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 748 5.25 %
Rwork0.1635 13490 -
obs0.1651 14238 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.59 Å2 / Biso mean: 30.3037 Å2 / Biso min: 9.09 Å2
Refinement stepCycle: final / Resolution: 1.63→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 65 82 1137
Biso mean--20.31 37.14 -
Num. residues----123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.63-1.760.25271480.20422674282298
1.76-1.930.21361560.17452724288099
1.93-2.210.19811360.14962686282299
2.21-2.790.17451390.16472709284898
2.79-30.260.19271690.15922697286698
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)
16.3586-3.6066-2.1597.39621.9684.35070.06240.18340.3271-0.0141-0.0762-0.0701-0.48640.0175-0.1070.152-0.0154-0.01850.1820.01850.1261-4.3241-0.866130.153
21.98151.53940.17593.1174-1.38493.414-0.165-0.1971-0.1442-0.17270.1972-0.14390.68990.46410.11740.16630.05150.01870.227-0.03660.26082.8852-16.96618.2451
31.3785-0.7391-0.4241.6648-0.31513.8434-0.03990.0976-0.3502-0.0756-0.00010.0950.29180.0796-0.00290.128-0.0069-0.00050.1613-0.04110.1709-2.2373-12.70713.5615
40.6654-0.0302-1.15582.0887-2.17324.38070.1342-0.4806-0.01910.3378-0.1629-0.2987-0.44461.25880.13270.2411-0.1455-0.01920.4141-0.01490.21986.9223.884313.0441
54.3460.2679-1.50763.97050.55384.7449-0.10.18890.1027-0.3285-0.0656-0.1837-0.14150.19710.10410.1941-0.0112-0.01520.2587-0.00150.1752-0.3511-2.89195.4468
66.97776.6821-5.59396.908-5.83324.93150.3893-0.23380.65030.2745-0.17660.2567-0.96120.0372-0.16630.3311-0.02460.00870.2232-0.01770.2306-1.74647.71546.2976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 28 )A7 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 40 )A29 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 92 )A41 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 101 )A93 - 101
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 114 )A102 - 114
6X-RAY DIFFRACTION6chain 'A' and (resid 115 through 129 )A115 - 129

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