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- PDB-5n1x: Crystal structure of the BCL6 BTB domain in complex with pyrazolo... -

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Basic information

Entry
Database: PDB / ID: 5n1x
TitleCrystal structure of the BCL6 BTB domain in complex with pyrazolo-pyrimidine ligand
Components(B-cell lymphoma 6 protein) x 3
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 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 / erythrocyte development / Rho protein signal transduction / regulation of immune response / 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 / protein localization / cell morphogenesis / 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 / metal ion binding / nucleus
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-8HH / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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: 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
C: B-cell lymphoma 6 protein
D: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5958
Polymers55,6384
Non-polymers9574
Water2,576143
1
A: B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)13,9811
Polymers13,9811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4603
Polymers13,9811
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2212
Polymers13,9811
Non-polymers2391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9332
Polymers13,6941
Non-polymers2391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.936, 47.936, 198.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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: 13981.269 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 / Production host: Komagataella pastoris (fungus) / References: UniProt: P41182
#2: 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: 13981.270 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
#3: 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: 13693.934 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 / Production host: Komagataella pastoris (fungus) / References: UniProt: P41182
#4: Chemical
ChemComp-8HH / ~{N}-ethyl-5-pyridin-3-yl-pyrazolo[1,5-a]pyrimidin-7-amine


Mass: 239.276 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H13N5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
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: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→198.95 Å / Num. obs: 47127 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 28.76 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22
Reflection shellResolution: 1.72→1.89 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.11.5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→49.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9373 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 2378 5.06 %RANDOM
Rwork0.1825 ---
obs0.1841 47040 99.36 %-
Displacement parametersBiso mean: 34.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.3742 Å20 Å20 Å2
2--1.3742 Å20 Å2
3----2.7483 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 1.72→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 72 143 4113
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014036HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.955448HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1466SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes673HARMONIC5
X-RAY DIFFRACTIONt_it4036HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion16.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion534SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4695SEMIHARMONIC4
LS refinement shellResolution: 1.72→1.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 162 5.06 %
Rwork0.2026 3037 -
all0.2039 3199 -
obs--99.36 %
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)
11.02580.0358-0.45890.8953-0.55841.5266-0.00390.0118-0.04420.02180.00530.03580.0201-0.0826-0.0015-0.01330.06890.01520.0037-0.0058-0.0595-18.81698.1914-0.7932
21.7706-0.4438-1.10360.5683-0.05062.1016-0.03190.14390.0792-0.01790.0288-0.0044-0.0154-0.02560.0031-0.02010.0733-0.0035-0.00350.005-0.0629-9.727718.6395-20.4076
30.6483-0.0608-0.66520.6229-0.25961.32480.08040.14250.0883-0.0446-0.0851-0.0311-0.1093-0.02820.00470.02090.11930.0120.03060.033-0.0621-35.2499-8.2729-20.3629
40.769-0.6532-0.38871.5991-0.37660.92920.10550.0793-0.0498-0.0423-0.14830.14150.02490.02970.0428-0.01990.0655-0.01440.0071-0.0252-0.0379-45.424-17.508-0.8841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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