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- PDB-6rjl: Fragment AZ-018 binding at the TAZpS89/14-3-3 sigma interface -

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Basic information

Entry
Database: PDB / ID: 6rjl
TitleFragment AZ-018 binding at the TAZpS89/14-3-3 sigma interface
Components
  • 14-3-3 protein sigma
  • TAZpS89
KeywordsPEPTIDE BINDING PROTEIN / protein protein interaction / fragment soaking / 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 / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / stem cell division / tissue homeostasis / hippo signaling ...kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / Physiological factors / RUNX3 regulates YAP1-mediated transcription / mesenchymal cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / stem cell division / tissue homeostasis / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / glomerulus development / SMAD protein signal transduction / Signaling by Hippo / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of fat cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / Regulation of localization of FOXO transcription factors / cilium assembly / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / positive regulation of epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / establishment of skin barrier / positive regulation of osteoblast differentiation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / 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 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TP53 Regulates Metabolic Genes / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of protein kinase activity / negative regulation of canonical Wnt signaling pathway / multicellular organism growth / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / osteoblast differentiation / positive regulation of protein localization to nucleus / transcription corepressor activity / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / transcription regulator complex / transcription coactivator activity / protein ubiquitination / nuclear body / regulation of cell cycle / 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 proteins signature 1. ...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
Chem-K5Z / 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: 1.28 Å
AuthorsGenet, S. / Wolter, M. / Guillory, X. / Somsen, B. / Leysen, S. / Patel, J. / Castaldi, P. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission Netherlands
CitationJournal: J.Med.Chem. / Year: 2020
Title: Fragment-based Differential Targeting of PPI Stabilizer Interfaces.
Authors: Guillory, X. / Wolter, M. / Leysen, S. / Neves, J.F. / Kuusk, A. / Genet, S. / Somsen, B. / Morrow, J.K. / Rivers, E. / van Beek, L. / Patel, J. / Goodnow, R. / Schoenherr, H. / Fuller, N. / ...Authors: Guillory, X. / Wolter, M. / Leysen, S. / Neves, J.F. / Kuusk, A. / Genet, S. / Somsen, B. / Morrow, J.K. / Rivers, E. / van Beek, L. / Patel, J. / Goodnow, R. / Schoenherr, H. / Fuller, N. / Cao, Q. / Doveston, R.G. / Brunsveld, L. / Arkin, M.R. / Castaldi, P. / Boyd, H. / Landrieu, I. / Chen, H. / Ottmann, C.
History
DepositionApr 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 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: 14-3-3 protein sigma
P: TAZpS89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8923
Polymers29,6332
Non-polymers2591
Water6,323351
1
A: 14-3-3 protein sigma
P: TAZpS89
hetero molecules

A: 14-3-3 protein sigma
P: TAZpS89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7856
Polymers59,2664
Non-polymers5192
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5780 Å2
ΔGint-36 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.200, 112.390, 62.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 (E. coli) / References: UniProt: P31947
#2: Protein/peptide TAZpS89


Mass: 1422.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9GZV5*PLUS
#3: Chemical ChemComp-K5Z / 5-(3-azanylpropyl)-4-phenyl-thiophene-2-carboximidamide


Mass: 259.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.095 M Na-HEPES pH 7.1, 27% PEG400, 0.19 M Calcium chloride, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.28→62.74 Å / Num. obs: 74931 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.997 / Rrim(I) all: 0.101 / Net I/σ(I): 14.2
Reflection shellResolution: 1.28→1.3 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3674 / CC1/2: 0.767 / Rrim(I) all: 1.003

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHR

3mhr


Resolution: 1.28→56.195 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.1
RfactorNum. reflection% reflection
Rfree0.1968 3669 4.9 %
Rwork0.1721 --
obs0.1733 74863 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.28→56.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 18 351 2297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092062
X-RAY DIFFRACTIONf_angle_d0.8912786
X-RAY DIFFRACTIONf_dihedral_angle_d15.378795
X-RAY DIFFRACTIONf_chiral_restr0.057301
X-RAY DIFFRACTIONf_plane_restr0.006367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.29680.25191460.25122683X-RAY DIFFRACTION100
1.2968-1.31460.25861420.2362738X-RAY DIFFRACTION100
1.3146-1.33340.23911580.22952665X-RAY DIFFRACTION100
1.3334-1.35330.2381390.23072713X-RAY DIFFRACTION100
1.3533-1.37440.25191170.23242750X-RAY DIFFRACTION100
1.3744-1.3970.22381590.21792712X-RAY DIFFRACTION100
1.397-1.42110.2141400.2162723X-RAY DIFFRACTION100
1.4211-1.44690.23841290.20692678X-RAY DIFFRACTION100
1.4469-1.47470.22661430.19092718X-RAY DIFFRACTION100
1.4747-1.50490.21461450.18182693X-RAY DIFFRACTION100
1.5049-1.53760.21861290.18182760X-RAY DIFFRACTION100
1.5376-1.57330.19361430.17362705X-RAY DIFFRACTION100
1.5733-1.61270.1681160.16872778X-RAY DIFFRACTION100
1.6127-1.65630.20391640.17142692X-RAY DIFFRACTION100
1.6563-1.7050.20761360.16432735X-RAY DIFFRACTION100
1.705-1.76010.20191380.17352722X-RAY DIFFRACTION100
1.7601-1.8230.2091320.16722722X-RAY DIFFRACTION100
1.823-1.8960.19311530.18072740X-RAY DIFFRACTION100
1.896-1.98230.19231380.17842739X-RAY DIFFRACTION100
1.9823-2.08680.18031430.16072741X-RAY DIFFRACTION100
2.0868-2.21750.16891620.15282729X-RAY DIFFRACTION100
2.2175-2.38880.18631560.15362721X-RAY DIFFRACTION99
2.3888-2.62910.16051270.15322788X-RAY DIFFRACTION100
2.6291-3.00960.18221170.16282807X-RAY DIFFRACTION100
3.0096-3.79160.1861280.15262829X-RAY DIFFRACTION100
3.7916-56.24920.21341690.17672913X-RAY DIFFRACTION100

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