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- PDB-6tbt: Crystal structure of the BCL6 BTB domain in complex with an Apt48... -

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Basic information

Entry
Database: PDB / ID: 6tbt
TitleCrystal structure of the BCL6 BTB domain in complex with an Apt48 peptide
Components
  • Apt48 peptide
  • B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / BCL6 / Apt48
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 / type 2 immune response / regulation of immune system process / 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 / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of cell differentiation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / 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 / nucleus / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZacharchenko, T. / Wright, S.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Kay Kendall Leukaemia FundKKLF1047 United Kingdom
CitationJournal: Structure / Year: 2021
Title: Structural basis of Apt48 inhibition of the BCL6 BTB domain.
Authors: Zacharchenko, T. / Kalverda, A.P. / Wright, S.C.
History
DepositionNov 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_refine_tls_group
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_refine_tls_group.beg_auth_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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: Apt48 peptide
D: Apt48 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,33413
Polymers31,9934
Non-polymers3419
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-118 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.630, 65.630, 156.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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: 14498.781 Da / Num. of mol.: 2 / Mutation: C8Q, C67R, C84N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21* (pLysS) / References: UniProt: P41182
#2: Protein/peptide Apt48 peptide


Mass: 1497.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 307 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M NaCl, 0.1 M Tris pH 7, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.558
11-h,-k,l20.442
ReflectionResolution: 1.63→78.2 Å / Num. obs: 49659 / % possible obs: 100 % / Redundancy: 19.39 % / CC1/2: 0.9986 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.027 / Net I/σ(I): 15.9
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 19.98 % / Rmerge(I) obs: 1.77 / Num. unique obs: 3390 / CC1/2: 0.51 / Rpim(I) all: 0.403 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R2B

1r2b


Resolution: 1.63→56.84 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.485 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 2515 5.1 %RANDOM
Rwork0.1527 ---
obs0.154 47080 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.21 Å2 / Biso mean: 26.591 Å2 / Biso min: 13.09 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å20 Å2
2--4.3 Å20 Å2
3----8.6 Å2
Refinement stepCycle: final / Resolution: 1.63→56.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 14 298 2402
Biso mean--35.24 39.23 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192164
X-RAY DIFFRACTIONr_bond_other_d0.0010.022130
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9532922
X-RAY DIFFRACTIONr_angle_other_deg0.93534861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39323.084107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33115402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2061522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 188 -
Rwork0.391 3390 -
all-3578 -
obs--99.92 %
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)
10.23680.111-0.1770.0918-0.0050.3061-0.01010.0510.01490.01560.05660.00660.03320.0341-0.04640.02340.01010.01920.0412-0.01080.0639.016219.99672.5522
20.3292-0.1372-0.31970.15810.01860.441-0.0273-0.0588-0.00110.01060.06040.03190.03260.0197-0.03310.03540.01710.02660.02780.01520.063426.952219.501823.5353
32.56650.58032.42565.63791.55572.4768-0.03820.0524-0.06190.35380.1115-0.10990.0310.0676-0.07330.05360.00610.02380.0031-0.00380.037736.66362.18111.7802
40.0965-0.7712-0.00796.19540.06320.00130.0071-0.00760.0041-0.22690.0175-0.046-0.0027-0.0014-0.02460.05160.03130.02170.02790.03110.090729.42411.726923.8382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 129
2X-RAY DIFFRACTION2B7 - 129
3X-RAY DIFFRACTION3C1 - 6
4X-RAY DIFFRACTION4D1 - 6

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