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- PDB-8r0z: 14-3-3 sigma in complex with TAZ peptide and stabilizing fragment... -

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Basic information

Entry
Database: PDB / ID: 8r0z
Title14-3-3 sigma in complex with TAZ peptide and stabilizing fragment TCF199
Components
  • 14-3-3 protein sigma
  • WW domain-containing transcription regulator protein 1
KeywordsSIGNALING PROTEIN / protein complex / stabilization
Function / homology
Function and homology information


kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / Physiological factors / RUNX3 regulates YAP1-mediated transcription / mesenchymal cell differentiation / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / stem cell division / hippo signaling / tissue homeostasis ...kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / Physiological factors / RUNX3 regulates YAP1-mediated transcription / mesenchymal cell differentiation / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / stem cell division / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / SMAD protein signal transduction / glomerulus development / Signaling by Hippo / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of epidermal cell division / protein kinase C inhibitor activity / negative regulation of fat cell differentiation / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / cilium assembly / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of osteoblast differentiation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of epithelial to mesenchymal transition / negative regulation of stem cell proliferation / positive regulation of protein localization / RHO GTPases activate PKNs / protein sequestering activity / protein kinase A signaling / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / negative regulation of protein phosphorylation / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Downregulation of SMAD2/3:SMAD4 transcriptional activity / transcription coregulator activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of protein kinase activity / negative regulation of canonical Wnt signaling pathway / multicellular organism growth / positive regulation of protein localization to nucleus / osteoblast differentiation / transcription corepressor activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / transcription regulator complex / transcription coactivator activity / nuclear body / regulation of cell cycle / protein ubiquitination / cadherin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...: / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein
Similarity search - Domain/homology
: / 14-3-3 protein sigma / WW domain-containing transcription regulator protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsCentorrino, F. / Andlovic, B. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: Biochemistry / Year: 2024
Title: Fragment-Based Interrogation of the 14-3-3/TAZ Protein-Protein Interaction.
Authors: Andlovic, B. / Valenti, D. / Centorrino, F. / Picarazzi, F. / Hristeva, S. / Hiltmann, M. / Wolf, A. / Cantrelle, F.X. / Mori, M. / Landrieu, I. / Levy, L.M. / Klebl, B. / Tzalis, D. / ...Authors: Andlovic, B. / Valenti, D. / Centorrino, F. / Picarazzi, F. / Hristeva, S. / Hiltmann, M. / Wolf, A. / Cantrelle, F.X. / Mori, M. / Landrieu, I. / Levy, L.M. / Klebl, B. / Tzalis, D. / Genski, T. / Eickhoff, J. / Ottmann, C.
History
DepositionNov 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7236
Polymers29,3622
Non-polymers3614
Water6,287349
1
A: 14-3-3 protein sigma
P: WW domain-containing transcription regulator protein 1
hetero molecules

A: 14-3-3 protein sigma
P: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,44612
Polymers58,7234
Non-polymers7238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)81.474, 111.984, 62.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28210.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P31947
#2: Protein/peptide WW domain-containing transcription regulator protein 1 / Transcriptional coactivator with PDZ-binding motif


Mass: 1151.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9GZV5
#3: Chemical ChemComp-XJF / [(4aR,8aR)-2,3,4,5,6,7,8,8a-octahydro-1H-quinolin-4a-yl]methyl N-phenylcarbamate


Mass: 288.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095M HEPES pH 7.5, 26%PEG 400, 0.19M CaCL, 5%Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.2→65.88 Å / Num. obs: 89634 / % possible obs: 99.98 % / Redundancy: 12.8 % / Biso Wilson estimate: 9.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.081 / Net I/σ(I): 17.4
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.529 / Num. unique obs: 8853 / CC1/2: 0.94 / Rrim(I) all: 0.575

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
MOLREPphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→65.88 Å / SU ML: 0.0918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.5907 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1756 4474 4.99 %
Rwork0.1687 85147 -
obs0.169 89621 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.26 Å2
Refinement stepCycle: LAST / Resolution: 1.2→65.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 24 349 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762044
X-RAY DIFFRACTIONf_angle_d0.91112771
X-RAY DIFFRACTIONf_chiral_restr0.0611305
X-RAY DIFFRACTIONf_plane_restr0.0057360
X-RAY DIFFRACTIONf_dihedral_angle_d22.9406806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.21361500.21362808X-RAY DIFFRACTION100
1.21-1.230.22391490.21112800X-RAY DIFFRACTION99.9
1.23-1.240.22091760.21442764X-RAY DIFFRACTION99.97
1.24-1.260.22071570.21332846X-RAY DIFFRACTION100
1.26-1.280.19631640.19692740X-RAY DIFFRACTION99.97
1.28-1.290.18021500.19352818X-RAY DIFFRACTION100
1.29-1.310.18031590.18962815X-RAY DIFFRACTION99.97
1.31-1.330.20771370.18652814X-RAY DIFFRACTION100
1.33-1.350.21711490.19412826X-RAY DIFFRACTION99.97
1.35-1.370.20261450.19272827X-RAY DIFFRACTION100
1.37-1.40.19311330.19212796X-RAY DIFFRACTION100
1.4-1.420.19761410.1872841X-RAY DIFFRACTION100
1.42-1.450.18541470.18052811X-RAY DIFFRACTION100
1.45-1.480.15871290.17122855X-RAY DIFFRACTION100
1.48-1.510.17951350.17092850X-RAY DIFFRACTION99.97
1.51-1.550.18541410.16922802X-RAY DIFFRACTION100
1.55-1.590.16651460.1672846X-RAY DIFFRACTION100
1.59-1.630.17621710.16772806X-RAY DIFFRACTION100
1.63-1.680.19181580.16452803X-RAY DIFFRACTION100
1.68-1.730.16161680.16522854X-RAY DIFFRACTION100
1.73-1.790.16631460.16762834X-RAY DIFFRACTION100
1.79-1.860.17051460.17112827X-RAY DIFFRACTION100
1.86-1.950.16281290.16562874X-RAY DIFFRACTION100
1.95-2.050.15791520.16052836X-RAY DIFFRACTION100
2.05-2.180.14521590.14892854X-RAY DIFFRACTION100
2.18-2.350.16771580.14932849X-RAY DIFFRACTION100
2.35-2.590.16931440.15212882X-RAY DIFFRACTION100
2.59-2.960.16531170.16592917X-RAY DIFFRACTION100
2.96-3.730.15341540.15942923X-RAY DIFFRACTION100
3.73-65.880.19911640.17043029X-RAY DIFFRACTION99.94

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