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- PDB-3lbz: Crystal Structure of the BCL6 BTB domain complexed with the small... -

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Basic information

Entry
Database: PDB / ID: 3lbz
TitleCrystal Structure of the BCL6 BTB domain complexed with the small molecule inhibitor 79-6
ComponentsB-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / Transcription regulation
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 / regulation of cell differentiation / regulation of T cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / negative regulation of cellular senescence / negative regulation of cell-matrix adhesion / negative regulation of Notch signaling pathway / Rho protein signal transduction / regulation of immune response / erythrocyte development / positive regulation of B cell proliferation / positive regulation of neuron differentiation / regulation of cytokine production / cell-matrix adhesion / transcription corepressor binding / cell motility / negative regulation of cell growth / cell morphogenesis / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / intracellular protein localization / heterochromatin formation / regulation of cell population proliferation / actin cytoskeleton organization / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / spermatogenesis / sequence-specific DNA binding / transcription by RNA polymerase II / positive regulation of apoptotic process / inflammatory response / 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 / negative regulation of transcription by RNA polymerase II / Golgi apparatus / zinc ion binding / nucleoplasm / identical protein 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 / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-[(4-bromophenyl)sulfonyl]acetamide / Chem-Z89 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGhetu, A.F. / Prive, G.G.
CitationJournal: Cancer Cell / Year: 2010
Title: A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo.
Authors: Cerchietti, L.C. / Ghetu, A.F. / Zhu, X. / Da Silva, G.F. / Zhong, S. / Matthews, M. / Bunting, K.L. / Polo, J.M. / Fares, C. / Arrowsmith, C.H. / Yang, S.N. / Garcia, M. / Coop, A. / ...Authors: Cerchietti, L.C. / Ghetu, A.F. / Zhu, X. / Da Silva, G.F. / Zhong, S. / Matthews, M. / Bunting, K.L. / Polo, J.M. / Fares, C. / Arrowsmith, C.H. / Yang, S.N. / Garcia, M. / Coop, A. / Mackerell, A.D. / Prive, G.G. / Melnick, A.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)31,0487
Polymers29,1202
Non-polymers1,9285
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-25 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.712, 38.611, 78.817
Angle α, β, γ (deg.)90.00, 114.70, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 2 / Auth seq-ID: 10 - 110 / Label seq-ID: 8 - 108

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein B-cell lymphoma 6 protein / BCL-6 / Zinc finger protein 51 / LAZ-3 protein / BCL-5 / Zinc finger and BTB domain-containing protein 27


Mass: 14559.823 Da / Num. of mol.: 2 / Fragment: BTB domain, residues 5-129 / Mutation: C8Q, C67R, C84N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL5, BCL6, LAZ3, ZBTB27, ZNF51 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3) / References: UniProt: P41182
#2: Chemical ChemComp-Z88 / N-[(4-bromophenyl)sulfonyl]acetamide


Mass: 278.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8BrNO3S
#3: Chemical ChemComp-Z89 / (2R)-2-[(5Z)-5-(5-bromo-2-oxo-1,2-dihydro-3H-indol-3-ylidene)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]butanedioic acid / N-[(1S)-2-AMINO-1-(2,4-DICHLOROBENZYL)ETHYL]-5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]THIOPHENE-2-CARBOXAMIDE


Mass: 457.276 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H9BrN2O6S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLIGAND Z89 A 201 AT SITE AC2 AND LIGAND Z89 A 202 AT SITE AC3 ARE AT ROUGHLY EQUIVALENT POSITIONS ...LIGAND Z89 A 201 AT SITE AC2 AND LIGAND Z89 A 202 AT SITE AC3 ARE AT ROUGHLY EQUIVALENT POSITIONS IN THE LATERAL GROOVE OF THE BCL6 BTB DOMAIN HOMODIMER

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 1 microliter of protein solution (9.5 mg/ml BCL6-BTB in 20 mM Tris pH 8.3, 450 mM NaCl, 1 mM TCEP) was mixed with 1 microliter of reservoir solution (180 mM sodium acetate, 190 mM sodium ...Details: 1 microliter of protein solution (9.5 mg/ml BCL6-BTB in 20 mM Tris pH 8.3, 450 mM NaCl, 1 mM TCEP) was mixed with 1 microliter of reservoir solution (180 mM sodium acetate, 190 mM sodium formate, 10% Glycerol, 50 mM NaCl and 10mM N-(4-bromophenylsulfonyl)acetamide), VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2006
Details: Rosenbaum-Rock double-crystal monochromator. Rosenbaum-Rock vertical focusing mirror.
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→46.225 Å / Num. all: 12478 / Num. obs: 12353 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 49.41 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.052 / Net I/σ(I): 17.86
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 11.36 / Num. unique all: 1684 / Rsym value: 0.14 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R29

1r29


Resolution: 2.3→46.225 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.7 / SU B: 7.99 / SU ML: 0.192 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 605 4.8 %RANDOM
Rwork0.2128 ---
all0.2154 12477 --
obs0.2154 -98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.94 Å2 / Biso mean: 42.93 Å2 / Biso min: 16.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å2-1.16 Å2
2--4.13 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 106 22 2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222110
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9292.0182860
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70323.12596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2211520
X-RAY DIFFRACTIONr_chiral_restr0.1480.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021573
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.2919
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21463
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.8610.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6911.51351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.70922017
X-RAY DIFFRACTIONr_scbond_it3.8531117
X-RAY DIFFRACTIONr_scangle_it6.6284.5843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
404tight positional0.090.05
408medium positional0.190.5
404tight thermal0.290.5
408medium thermal1.242
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 39 -
Rwork0.209 862 -
obs-904 98.47 %

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