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- PDB-5x9p: Crystal structure of the BCL6 BTB domain in complex with Compound 5 -

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Basic information

Entry
Database: PDB / ID: 5x9p
TitleCrystal structure of the BCL6 BTB domain in complex with Compound 5
ComponentsB-cell lymphoma 6 protein
KeywordsTranscription/Inhibitor / Transcription Repressor / Transcription-Inhibitor complex
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
Chem-80L / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSogabe, S. / Ida, K. / Lane, W. / Snell, G.
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design
Authors: Yasui, T. / Yamamoto, T. / Sakai, N. / Asano, K. / Takai, T. / Yoshitomi, Y. / Davis, M. / Takagi, T. / Sakamoto, K. / Sogabe, S. / Kamada, Y. / Lane, W. / Snell, G. / Iwata, M. / Goto, M. / ...Authors: Yasui, T. / Yamamoto, T. / Sakai, N. / Asano, K. / Takai, T. / Yoshitomi, Y. / Davis, M. / Takagi, T. / Sakamoto, K. / Sogabe, S. / Kamada, Y. / Lane, W. / Snell, G. / Iwata, M. / Goto, M. / Inooka, H. / Sakamoto, J.I. / Nakada, Y. / Imaeda, Y.
History
DepositionMar 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6792
Polymers16,2881
Non-polymers3921
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9050 Å2
2
A: B-cell lymphoma 6 protein
hetero molecules

A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3594
Polymers32,5752
Non-polymers7842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area3920 Å2
ΔGint-38 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.550, 66.550, 153.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-916-

HOH

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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: 16287.733 Da / Num. of mol.: 1 / Fragment: UNP residues 5-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P41182
#2: Chemical ChemComp-80L / 3-[[4-chloranyl-2-nitro-5-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)amino]phenyl]amino]propanoic acid / N-(4-chloro-2-nitro-5-((2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)amino)phenyl)-beta-alanine


Mass: 391.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14ClN5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis-Tris, potassium/sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 17116 / % possible obs: 96.6 % / Redundancy: 10.6 % / Rsym value: 0.063 / Net I/σ(I): 37.8
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2 / Rsym value: 1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R28

1r28


Resolution: 1.86→40 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.93 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23463 866 5.1 %RANDOM
Rwork0.18888 ---
obs0.1911 16233 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.86→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 27 56 1133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191095
X-RAY DIFFRACTIONr_bond_other_d0.0010.021019
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9891480
X-RAY DIFFRACTIONr_angle_other_deg1.01732348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8075130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41623.52951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85415195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.603159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6473.297523
X-RAY DIFFRACTIONr_mcbond_other1.6483.289522
X-RAY DIFFRACTIONr_mcangle_it2.6094.923652
X-RAY DIFFRACTIONr_mcangle_other2.6084.931653
X-RAY DIFFRACTIONr_scbond_it2.2663.773572
X-RAY DIFFRACTIONr_scbond_other2.2593.771571
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7545.526829
X-RAY DIFFRACTIONr_long_range_B_refined5.18438.8461220
X-RAY DIFFRACTIONr_long_range_B_other5.16938.8141220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.859→1.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 70 -
Rwork0.264 1173 -
obs--98.81 %
Refinement TLS params.Method: refined / Origin x: 30.7192 Å / Origin y: -23.8867 Å / Origin z: -3.6731 Å
111213212223313233
T0.0222 Å2-0.0127 Å20.0076 Å2-0.0907 Å20.0675 Å2--0.0686 Å2
L0.5343 °2-0.0057 °2-0.3502 °2-0.3178 °2-0.6528 °2--1.6465 °2
S-0.0033 Å °-0.0901 Å °-0.0445 Å °-0.0088 Å °-0.0171 Å °-0.0265 Å °0.0173 Å °0.0244 Å °0.0203 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION1A801

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