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- PDB-6y17: Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with... -

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Basic information

Entry
Database: PDB / ID: 6y17
TitleCrystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with nebulinSH3-NCoR1BBD1
Components
  • Nebulin,Nuclear receptor corepressor 1
  • Nuclear receptor corepressor 1,B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / BCL6 / NCoR1.
Function / homology
Function and homology information


cardiac muscle thin filament assembly / regulation of actin filament length / somatic muscle development / : / 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 ...cardiac muscle thin filament assembly / regulation of actin filament length / somatic muscle development / : / 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 / Striated Muscle Contraction / 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 / structural constituent of muscle / 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 / muscle organ development / 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 / histone deacetylase complex / regulation of T cell proliferation / B cell proliferation / 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 / spindle assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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 / NOTCH1 Intracellular Domain Regulates Transcription / Transcriptional regulation of white adipocyte differentiation / 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 / Z disc / cell morphogenesis / HCMV Early Events / sequence-specific double-stranded DNA binding / actin filament binding / mitotic spindle / : / transcription corepressor activity / intracellular protein localization / heterochromatin formation / actin cytoskeleton / regulation of cell population proliferation / actin binding / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / regulation of inflammatory response / actin cytoskeleton organization / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / DNA-binding transcription factor binding / sequence-specific DNA binding
Similarity search - Function
Nebulin-like / Nebulin, SH3 domain / : / Nebulin repeat / Nebulin repeat / Nebulin repeat profile. / NEBU / N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain ...Nebulin-like / Nebulin, SH3 domain / : / Nebulin repeat / Nebulin repeat / Nebulin repeat profile. / NEBU / N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Variant SH3 domain / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / SH3 Domains / 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 / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Nebulin / Nuclear receptor corepressor 1 / Nebulin / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 11, 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: Nuclear receptor corepressor 1,B-cell lymphoma 6 protein
B: Nuclear receptor corepressor 1,B-cell lymphoma 6 protein
C: Nebulin,Nuclear receptor corepressor 1
D: Nebulin,Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9575
Polymers48,9344
Non-polymers231
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-58 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.460, 47.303, 59.781
Angle α, β, γ (deg.)95.865, 95.600, 94.205
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Nuclear receptor corepressor 1,B-cell lymphoma 6 protein / N-CoR1 / BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain- ...N-CoR1 / 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: 15602.981 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOR1, KIAA1047, BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: O75376, UniProt: P41182
#2: Protein Nebulin,Nuclear receptor corepressor 1 / N-CoR1


Mass: 8864.005 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEB, NCOR1, KIAA1047 / Production host: Escherichia coli (E. coli)
References: UniProt: H0Y786, UniProt: O75376, UniProt: P20929*PLUS
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.25 Å3/Da / Density % sol: 45.32 % / Description: Large rods
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.66 M ammonium sulfate, 3.3% (v/v) glycerol, 0.05 M magnesium sulfate, 0.1 M imidazole/ hydrochloric acid pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96884 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96884 Å / Relative weight: 1
ReflectionResolution: 1.56→46.88 Å / Num. obs: 58832 / % possible obs: 96.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.31 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.105 / Net I/σ(I): 5.5
Reflection shellResolution: 1.56→1.6 Å / Rmerge(I) obs: 1.157 / Num. unique obs: 4261 / CC1/2: 0.383 / Rpim(I) all: 0.955 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R28

1r28


Resolution: 1.56→34.92 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.8641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2008 2878 4.9 %
Rwork0.1766 55826 -
obs0.1778 58704 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.55 Å2
Refinement stepCycle: LAST / Resolution: 1.56→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 1 362 3642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823345
X-RAY DIFFRACTIONf_angle_d0.94544514
X-RAY DIFFRACTIONf_chiral_restr0.0703512
X-RAY DIFFRACTIONf_plane_restr0.0062584
X-RAY DIFFRACTIONf_dihedral_angle_d13.11281250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.590.3041400.26892531X-RAY DIFFRACTION92.14
1.59-1.610.26191410.24272555X-RAY DIFFRACTION93.97
1.61-1.640.29461390.22232614X-RAY DIFFRACTION94.77
1.64-1.670.23091270.2242617X-RAY DIFFRACTION95.48
1.67-1.710.27221410.22312646X-RAY DIFFRACTION95.94
1.71-1.740.25251380.2062640X-RAY DIFFRACTION95.66
1.74-1.790.24861200.21822624X-RAY DIFFRACTION95.71
1.79-1.830.24671350.2042646X-RAY DIFFRACTION96.26
1.83-1.880.19251390.19862703X-RAY DIFFRACTION96.47
1.88-1.930.2831270.23862603X-RAY DIFFRACTION96.06
1.93-20.21831390.18832686X-RAY DIFFRACTION97.05
2-2.070.22291380.17762705X-RAY DIFFRACTION96.87
2.07-2.150.22891310.1732638X-RAY DIFFRACTION97.02
2.15-2.250.21171490.19252648X-RAY DIFFRACTION97.29
2.25-2.370.19791370.17622703X-RAY DIFFRACTION97.46
2.37-2.520.21311370.17812669X-RAY DIFFRACTION97.91
2.52-2.710.2211440.17372700X-RAY DIFFRACTION97.97
2.71-2.980.1981520.17552710X-RAY DIFFRACTION98.45
2.98-3.410.17121450.16462688X-RAY DIFFRACTION98.81
3.41-4.30.16061300.14282764X-RAY DIFFRACTION99.08
4.3-34.920.15651290.15122736X-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)
11.67307203022-0.279670251119-0.05809940705191.20946872327-0.5071793629311.897741076040.0368642360267-0.01390165558110.1229006992150.0883757710918-0.0760282769813-0.179456764015-0.02374632892690.09810643023650.01204851527040.0833045475894-0.00592409201481-0.002248572377470.065199128548-0.00357020726410.102966419501-13.000164276-53.897324912715.0708370552
21.971856559030.1243498135140.3118804651291.025387256890.1257823228451.383868406520.025330843030.205547609197-0.168001623947-0.005791428778210.01942315899980.1248677504820.141246909386-0.18879447957-0.05016585063450.09309448786450.01099374799020.00271224908880.141587572696-0.005231126284380.090801240669-27.6390276811-59.69492498053.66301389901
30.9445732750751.82256786056-2.652326609052.30522687287-3.847140755164.67806034809-0.1598710625320.009048689729150.0203625678359-0.2146486822940.1076392838960.02205775775830.326752858481-0.1726716031880.07960294364030.275952889903-0.0005853281382980.005494930387890.2190846271260.02329809246670.238698554496-21.6190552549-35.7435886583-22.8842644656
40.702487570585-0.893780138985-0.5029214839332.16431932831.624228941341.31416908294-0.0170465736723-0.1860185643070.065262186106-0.03994216402080.0165839685011-0.0468294300035-0.114778697142-0.03986878750330.01242307979140.141788442154-0.005266433397670.02064060991090.2210001003620.01181224059190.108040411261-19.9161111223-24.326738219132.8808393835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 128)
2X-RAY DIFFRACTION2(chain 'B' and resid -7 through 127)
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 80)
4X-RAY DIFFRACTION4(chain 'D' and resid -1 through 80)

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