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- PDB-6xxs: Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with... -

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Basic information

Entry
Database: PDB / ID: 6xxs
TitleCrystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with the NcoR1 BBD1 corepressor peptide.
Components
  • (B-cell lymphoma 6 protein) x 2
  • Nuclear receptor corepressor 1
KeywordsTRANSCRIPTION / BCL6 / NCoR1.
Function / homology
Function and homology information


: / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / 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 plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes ...: / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / 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 plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / negative regulation of glycolytic process / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / nuclear thyroid hormone receptor binding / pyramidal neuron differentiation / type 2 immune response / negative regulation of JNK cascade / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / positive regulation of cell motility / negative regulation of B cell apoptotic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fatty acid metabolic process / Notch-HLH transcription pathway / negative regulation of Rho protein signal transduction / erythrocyte development / FOXO-mediated transcription of cell death genes / locomotor rhythm / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of T cell proliferation / B cell proliferation / histone deacetylase complex / negative regulation of cellular senescence / Regulation of MECP2 expression and activity / negative regulation of cell-matrix adhesion / negative regulation of Notch signaling pathway / regulation of immune response / Nuclear signaling by ERBB4 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / spindle assembly / Rho protein signal transduction / positive regulation of B cell proliferation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / positive regulation of neuron differentiation / regulation of cytokine production / negative regulation of miRNA transcription / cell-matrix adhesion / nuclear receptor binding / transcription corepressor binding / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cell motility / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / negative regulation of cell growth / Cytoprotection by HMOX1 / chromatin DNA binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cell morphogenesis / HCMV Early Events / sequence-specific double-stranded DNA binding / mitotic spindle / : / transcription corepressor activity / intracellular protein localization / heterochromatin formation / regulation of cell population proliferation / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / actin cytoskeleton organization / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / DNA-binding transcription factor binding / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Zinc finger, C2H2 type / 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 / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / 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: 3.25 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 28, 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: B-cell lymphoma 6 protein
C: Nuclear receptor corepressor 1
D: Nuclear receptor corepressor 1
E: B-cell lymphoma 6 protein
G: Nuclear receptor corepressor 1
F: B-cell lymphoma 6 protein
H: Nuclear receptor corepressor 1


Theoretical massNumber of molelcules
Total (without water)68,7358
Polymers68,7358
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19840 Å2
ΔGint-110 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.380, 165.380, 244.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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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: 15488.877 Da / Num. of mol.: 3
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.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75376
#3: 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

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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: 7.14 Å3/Da / Density % sol: 82.76 %
Description: Rod like crystals, High-Solvent content, Porous lattice.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2M Sodium chloride 5%(w/v) PEG 4000 0.1M Tris base/ Hydrochloric acid pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.25→93.05 Å / Num. obs: 31807 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 72.67 Å2 / CC1/2: 0.958 / Rpim(I) all: 0.17 / Net I/σ(I): 5.5
Reflection shellResolution: 3.25→3.43 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4532 / CC1/2: 0.154 / Rpim(I) all: 0.818 / % possible all: 100

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Processing

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

1r28


Resolution: 3.25→82.69 Å / SU ML: 0.4326 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1610 5.07 %
Rwork0.1966 30166 -
obs0.198 31776 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.26 Å2
Refinement stepCycle: LAST / Resolution: 3.25→82.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4675 0 0 0 4675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00354764
X-RAY DIFFRACTIONf_angle_d0.5756425
X-RAY DIFFRACTIONf_chiral_restr0.0463756
X-RAY DIFFRACTIONf_plane_restr0.0036819
X-RAY DIFFRACTIONf_dihedral_angle_d16.96091827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.350.35741180.34042447X-RAY DIFFRACTION99.65
3.35-3.450.33441340.32442470X-RAY DIFFRACTION100
3.45-3.580.31671260.30422459X-RAY DIFFRACTION100
3.58-3.720.28171330.2622470X-RAY DIFFRACTION99.96
3.72-3.890.2671260.22392495X-RAY DIFFRACTION100
3.89-4.090.2611450.20552468X-RAY DIFFRACTION100
4.09-4.350.19121440.16412493X-RAY DIFFRACTION100
4.35-4.690.14771380.13472492X-RAY DIFFRACTION100
4.69-5.160.15131390.13152511X-RAY DIFFRACTION99.96
5.16-5.90.23591310.16062548X-RAY DIFFRACTION99.96
5.91-7.440.19741120.19592594X-RAY DIFFRACTION99.96
7.44-82.690.20881640.16862719X-RAY DIFFRACTION99.41
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)
12.962886733621.218885072031.632337128052.524398373910.5455193699072.628297285650.07611558202610.212854920273-0.130213666916-0.02570743023980.1669448470190.01172054046910.294397479286-0.109407784955-0.2496779248810.3754215022710.0203816435334-0.0006341447919970.48608535318-0.05243914011620.340176737173-71.548547871236.3347285051-46.6411398856
21.871214729330.08465539513150.7578130036681.575469562951.133453981395.549796126460.0831073649958-0.2380611799940.2079101596180.256868477663-0.0371700236749-0.160384563480.147771595029-0.121880584939-0.04520666751610.418309319531-0.0473954545934-0.02142750177520.419850935569-0.04133255929190.401718770688-62.28561934144.4822243587-34.8781383309
37.67281203209-0.217739987561-1.452326983015.773270515071.897446497595.93077979736-0.2139409890470.2216522832591.12673486071-0.177274972190.739156554975-0.272711825672-0.273767456245-0.268264030588-0.6022343476640.6435048886860.0069671414204-0.0265649122120.4255260997940.01339848947370.291737210891-68.835268482543.8845163879-54.1517529994
44.9064989564-0.0627577077280.9926010671615.159955695950.9130011171374.31910370410.03061980126350.3157114008060.125307114795-0.781301269960.203963985741-0.721586083028-0.02505943690821.19893807225-0.4167697448870.420830018314-0.110857181820.01384129152620.486139542284-0.1905792657250.534241143738-53.437811971144.1675969014-40.9787763971
56.314043135630.7153262479080.539760610233.580234425930.6622597385671.931927347980.02965359366660.0412954104513-0.08302743075140.2759042759690.102374539429-0.2028080098620.1284812086480.290356887723-0.1010146548560.5490154565740.049683593035-0.10507468470.393013358752-0.09018662428090.420243791781-63.4960866701-1.95668451533-57.5348669913
63.83644561357-3.044512845334.007944118864.18652814051-6.043888608288.794264643270.4434404566180.495581769776-0.7174628098521.02252815910.305757392118-0.328806018357-0.7605228886751.27985328908-0.7993002093280.8161653781250.03246911603230.01933532040790.594425577379-0.3688543183060.981740808421-52.2329968967-6.64005735831-59.6485386247
71.434064496541.185610053920.1633915358872.69720105817-0.03827046780111.40282245702-0.224853162440.1244049761430.1120367222920.01388436002930.426605612681-0.982542874481-0.09939948522430.52000189915-0.1654376371940.476375169156-0.0187388568982-0.0568993674280.692925148897-0.2418800088440.751151831184-51.229116308913.7269756445-53.8391749044
88.03836120552-5.45478686177-5.066031852074.22763331283.529691948213.29283820449-0.6294368043630.8603998468380.1664553164010.7099623729440.606039659738-0.9931994594011.28688953121-0.08254815985310.2526776149150.6851733247330.102062686088-0.1426001035181.06733996271-0.2965410825541.00831452074-44.44993727357.71544742814-47.2678548684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -2 through 127)
2X-RAY DIFFRACTION2(chain 'B' and resid -4 through 126)
3X-RAY DIFFRACTION3(chain 'C' and resid 1340 through 1356)
4X-RAY DIFFRACTION4(chain 'D' and resid 1341 through 1356)
5X-RAY DIFFRACTION5(chain 'E' and resid 6 through 127)
6X-RAY DIFFRACTION6(chain 'G' and resid 1340 through 1356)
7X-RAY DIFFRACTION7(chain 'F' and resid -2 through 126)
8X-RAY DIFFRACTION8(chain 'H' and resid 1341 through 1356)

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