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- PDB-5n21: Crystal structure of the BCL6 BTB domain in complex with pyrazolo... -

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Basic information

Entry
Database: PDB / ID: 5n21
TitleCrystal structure of the BCL6 BTB domain in complex with pyrazolo-pyrimidine ligand
ComponentsB-cell lymphoma 6 protein
KeywordsTRANSFERASE / KINASE
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
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8HN / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsRobb, G. / Ferguson, A. / Hargreaves, D.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors.
Authors: McCoull, W. / Abrams, R.D. / Anderson, E. / Blades, K. / Barton, P. / Box, M. / Burgess, J. / Byth, K. / Cao, Q. / Chuaqui, C. / Carbajo, R.J. / Cheung, T. / Code, E. / Ferguson, A.D. / ...Authors: McCoull, W. / Abrams, R.D. / Anderson, E. / Blades, K. / Barton, P. / Box, M. / Burgess, J. / Byth, K. / Cao, Q. / Chuaqui, C. / Carbajo, R.J. / Cheung, T. / Code, E. / Ferguson, A.D. / Fillery, S. / Fuller, N.O. / Gangl, E. / Gao, N. / Grist, M. / Hargreaves, D. / Howard, M.R. / Hu, J. / Kemmitt, P.D. / Nelson, J.E. / O'Connell, N. / Prince, D.B. / Raubo, P. / Rawlins, P.B. / Robb, G.R. / Shi, J. / Waring, M.J. / Whittaker, D. / Wylot, M. / Zhu, X.
History
DepositionFeb 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Data collection / Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1356
Polymers28,2012
Non-polymers9344
Water3,999222
1
A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5673
Polymers14,1001
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5673
Polymers14,1001
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.400, 38.970, 54.930
Angle α, β, γ (deg.)83.36, 75.39, 67.21
Int Tables number1
Space group name H-MP1

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Components

#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: 14100.413 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Komagataella pastoris (fungus) / References: UniProt: P41182
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-8HN / 2-[(2~{S})-1-[3-cyano-7-[(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)amino]pyrazolo[1,5-a]pyrimidin-5-yl]pyrrolidin-2-yl]ethanoic acid


Mass: 431.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21N7O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→35.92 Å / Num. obs: 29482 / % possible obs: 94.9 % / Redundancy: 2.1 % / Biso Wilson estimate: 20.89 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.4
Reflection shellResolution: 1.58→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2 / % possible all: 85.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.11.5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→19.83 Å / Cor.coef. Fo:Fc: 0.9598 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.089 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.085
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 1411 4.81 %RANDOM
Rwork0.1632 ---
obs0.1646 29307 95.15 %-
Displacement parametersBiso mean: 22.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.0437 Å21.4735 Å20.1491 Å2
2---3.9355 Å2-0.6701 Å2
3---1.8919 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: LAST / Resolution: 1.58→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 66 222 2275
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012092HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972836HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d782SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes358HARMONIC5
X-RAY DIFFRACTIONt_it2092HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion15.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion275SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2710SEMIHARMONIC4
LS refinement shellResolution: 1.58→1.64 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2228 130 5.19 %
Rwork0.1967 2374 -
all0.198 2504 -
obs--95.15 %
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)
10.3245-0.12940.01110.2875-0.08421.047-0.0203-0.11450.02130.05950.0105-0.0216-0.0869-0.10440.0098-0.04140.02050.0097-0.0384-0.0113-0.01720.51651.497-1.5613
20.45930.1599-0.00490.43410.02960.9126-0.04390.10770.037-0.06550.02260.0128-0.06720.08730.0212-0.0449-0.01450.0109-0.0466-0.0053-0.014812.3221.4643-21.1196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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