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- PDB-5mw6: Crystal structure of the BCL6 BTB-domain with compound 1 -

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Basic information

Entry
Database: PDB / ID: 5mw6
TitleCrystal structure of the BCL6 BTB-domain with compound 1
ComponentsB-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / Inhibitor
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 / plasma cell differentiation ...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 / plasma cell differentiation / paraspeckles / germinal center formation / negative regulation of leukocyte proliferation / 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 / erythrocyte development / 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 / 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 / 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-RC0 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsDavies, D.R. / Kessler, D.
CitationJournal: Cell Rep / Year: 2017
Title: Chemically Induced Degradation of the Oncogenic Transcription Factor BCL6.
Authors: Kerres, N. / Steurer, S. / Schlager, S. / Bader, G. / Berger, H. / Caligiuri, M. / Dank, C. / Engen, J.R. / Ettmayer, P. / Fischerauer, B. / Flotzinger, G. / Gerlach, D. / Gerstberger, T. / ...Authors: Kerres, N. / Steurer, S. / Schlager, S. / Bader, G. / Berger, H. / Caligiuri, M. / Dank, C. / Engen, J.R. / Ettmayer, P. / Fischerauer, B. / Flotzinger, G. / Gerlach, D. / Gerstberger, T. / Gmaschitz, T. / Greb, P. / Han, B. / Heyes, E. / Iacob, R.E. / Kessler, D. / Kolle, H. / Lamarre, L. / Lancia, D.R. / Lucas, S. / Mayer, M. / Mayr, K. / Mischerikow, N. / Muck, K. / Peinsipp, C. / Petermann, O. / Reiser, U. / Rudolph, D. / Rumpel, K. / Salomon, C. / Scharn, D. / Schnitzer, R. / Schrenk, A. / Schweifer, N. / Thompson, D. / Traxler, E. / Varecka, R. / Voss, T. / Weiss-Puxbaum, A. / Winkler, S. / Zheng, X. / Zoephel, A. / Kraut, N. / McConnell, D. / Pearson, M. / Koegl, M.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)29,6744
Polymers29,0062
Non-polymers6682
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-27 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.860, 33.010, 48.900
Angle α, β, γ (deg.)90.00, 94.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-124-

PHE

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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: 14502.771 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: Escherichia coli (E. coli) / References: UniProt: P41182
#2: Chemical ChemComp-RC0 / 5-chloranyl-~{N}-(4-chlorophenyl)-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-amine


Mass: 334.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13Cl2N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Na/K phosphate 20 % PEG 400 15 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.65→70.19 Å / Num. obs: 27226 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 1 % / Biso Wilson estimate: 21.66 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.84
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
RefinementResolution: 1.65→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.106 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1302 4.78 %RANDOM
Rwork0.181 ---
obs0.183 27221 99.4 %-
Displacement parametersBiso mean: 26.13 Å2
Baniso -1Baniso -2Baniso -3
1--10.3445 Å20 Å2-0.9106 Å2
2--6.7982 Å20 Å2
3---3.5463 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 44 153 2148
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082093HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.962845HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d780SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes318HARMONIC5
X-RAY DIFFRACTIONt_it2093HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion14.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion280SEMIHARMONIC5
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_contact2617SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.246 107 3.78 %
Rwork0.234 2722 -
all0.235 2829 -
obs--99.93 %
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)
11.2806-0.28790.230.32630.14080.85520.09850.2311-0.125-0.1209-0.07730.09030.0163-0.0955-0.0212-0.06220.0151-0.01850.0254-0.0507-0.028819.99051.86461.6799
21.5873-0.03260.17250.30220.26130.9241-0.052-0.09710.08760.022-0.02170.09170.0296-0.18590.0737-0.05950.0068-0.01-0.0048-0.0305-0.012616.454811.97922.7078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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