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

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Basic information

Entry
Database: PDB / ID: 6xyx
TitleCrystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD corepressor 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 / negative regulation of JNK cascade / 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 glycolytic process / 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 / negative regulation of Notch signaling pathway / regulation of cell differentiation / Notch-HLH transcription pathway / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / 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 / positive regulation of B cell proliferation / Nuclear signaling by ERBB4 / 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 / heterochromatin formation / PPARA activates gene expression / Cytoprotection by HMOX1 / negative regulation of cell growth / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / 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 / 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 / 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
Nuclear receptor corepressor 1 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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
DepositionJan 31, 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

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Assembly

Deposited unit
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
D: Nuclear receptor corepressor 1
C: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9907
Polymers32,8824
Non-polymers1083
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-63 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.660, 64.520, 137.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 14498.781 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: Protein/peptide Nuclear receptor corepressor 1 / N-CoR1


Mass: 1942.288 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOR1, KIAA1047 / Production host: Escherichia coli (E. coli) / References: UniProt: O75376
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium acetate trihydrate 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350

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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: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.44→68.88 Å / Num. obs: 56791 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Net I/σ(I): 9.1
Reflection shellResolution: 1.44→1.52 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8133 / CC1/2: 0.606 / Rpim(I) all: 0.894

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Processing

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

1r28


Resolution: 1.44→21.63 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.1978 2809 4.95 %
Rwork0.167 --
obs0.1686 56709 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.05 Å2 / Biso mean: 31.6561 Å2 / Biso min: 16.07 Å2
Refinement stepCycle: final / Resolution: 1.44→21.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 6 244 2442
Biso mean--46.21 42.88 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.460.34471280.318326372765100
1.46-1.490.34431510.285226362787100
1.49-1.520.30421230.260326622785100
1.52-1.550.26721350.246226582793100
1.55-1.580.2841360.21472664280099
1.58-1.620.26661450.190926422787100
1.62-1.660.22561310.17627192850100
1.66-1.710.20661660.17325992765100
1.71-1.760.20951200.163627032823100
1.76-1.810.20591600.150426662826100
1.81-1.880.20051180.147826972815100
1.88-1.950.16061320.14112659279199
1.95-2.040.20261420.160327002842100
2.04-2.150.19871150.150327392854100
2.15-2.290.20941300.150426982828100
2.29-2.460.19211630.15762684284799
2.46-2.710.18191470.164227302877100
2.71-3.10.22511590.179327282887100
3.1-3.90.17031610.15932755291699
3.9-21.630.18171470.161629243071100

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