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- PDB-6xzz: Crystal structure of the BCL6 BTB domain in complex with the NCoR... -

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Basic information

Entry
Database: PDB / ID: 6xzz
TitleCrystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD2 peptide
Components
  • B-cell lymphoma 6 protein
  • Nuclear receptor corepressor 1
KeywordsTRANSCRIPTION / BCL6 / NCoR1.
Function / homology
Function and homology information


NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / 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 androgen receptor signaling pathway ...NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / 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 androgen receptor signaling pathway / 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 / negative regulation of JNK cascade / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / negative regulation of glycolytic process / positive regulation of cell motility / nuclear thyroid hormone receptor binding / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / negative regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / regulation of T cell proliferation / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / negative regulation of Notch signaling pathway / Notch-HLH transcription pathway / B cell proliferation / locomotor rhythm / negative regulation of cellular senescence / histone deacetylase complex / Rho protein signal transduction / Regulation of MECP2 expression and activity / regulation of immune response / spindle assembly / erythrocyte development / Nuclear signaling by ERBB4 / positive regulation of B cell proliferation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / regulation of cytokine production / transcription repressor complex / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cell-matrix adhesion / transcription corepressor binding / negative regulation of miRNA transcription / nuclear receptor binding / cell motility / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / negative regulation of cell growth / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / heterochromatin formation / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / sequence-specific double-stranded DNA binding / protein localization / Circadian Clock / chromatin organization / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / inflammatory response / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / 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 / Homeobox-like domain superfamily
Similarity search - Domain/homology
trifluoroacetic acid / Nuclear receptor corepressor 1 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsZacharchenko, T. / Wright, S.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Kay Kendall Leukaemia FundKKLF1047 United Kingdom
CitationJournal: Iucrj / Year: 2021
Title: Functionalization of the BCL6 BTB domain into a noncovalent crystallization chaperone.
Authors: Zacharchenko, T. / Wright, S.
History
DepositionFeb 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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
B: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,71012
Polymers16,3642
Non-polymers34610
Water2,180121
1
A: B-cell lymphoma 6 protein
B: Nuclear receptor corepressor 1
hetero molecules

A: B-cell lymphoma 6 protein
B: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,41924
Polymers32,7284
Non-polymers69220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Unit cell
Length a, b, c (Å)67.014, 67.014, 152.016
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-405-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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.: 1
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: Protein/peptide Nuclear receptor corepressor 1 / N-CoR1


Mass: 1865.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75376

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Non-polymers , 4 types, 131 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 13.4%(v/v) PEG 400, 0.335M K2HPO4 / NaH2PO4 pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.39→54.22 Å / Num. obs: 41626 / % possible obs: 100 % / Redundancy: 18.3 % / Biso Wilson estimate: 14.57 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 13.2
Reflection shellResolution: 1.39→1.41 Å / Num. unique obs: 2036 / CC1/2: 0.524 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R28

1r28


Resolution: 1.39→54.22 Å / SU ML: 0.1804 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 2020 4.91 %
Rwork0.1846 39099 -
obs0.1857 41119 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.78 Å2
Refinement stepCycle: LAST / Resolution: 1.39→54.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 16 121 1202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511153
X-RAY DIFFRACTIONf_angle_d0.79471570
X-RAY DIFFRACTIONf_chiral_restr0.0834181
X-RAY DIFFRACTIONf_plane_restr0.0051204
X-RAY DIFFRACTIONf_dihedral_angle_d17.8462463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.40911160.36492684X-RAY DIFFRACTION96.49
1.42-1.460.35811240.30952732X-RAY DIFFRACTION98.58
1.46-1.510.2891380.27252729X-RAY DIFFRACTION98.93
1.51-1.550.31281380.25062750X-RAY DIFFRACTION99.07
1.55-1.610.29141400.22432762X-RAY DIFFRACTION99.32
1.61-1.670.23371430.20672759X-RAY DIFFRACTION99.35
1.67-1.750.25261560.19692739X-RAY DIFFRACTION99.11
1.75-1.840.22851520.17512768X-RAY DIFFRACTION99.42
1.84-1.960.22121600.1542747X-RAY DIFFRACTION98.74
1.96-2.110.20761440.15012806X-RAY DIFFRACTION99.19
2.11-2.320.14951480.14492799X-RAY DIFFRACTION99.06
2.32-2.660.17321550.16062832X-RAY DIFFRACTION99.2
2.66-3.350.16661440.17862906X-RAY DIFFRACTION99.58
3.35-54.220.19421620.18343086X-RAY DIFFRACTION99.6

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