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- PDB-6slw: Fragment AZ-004 binding at the TAZpS89/14-3-3 sigma interface -

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Basic information

Entry
Database: PDB / ID: 6slw
TitleFragment AZ-004 binding at the TAZpS89/14-3-3 sigma interface
Components
  • 14-3-3 protein sigma
  • WW domain-containing transcription regulator protein 1
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 / negative regulation of keratinocyte proliferation / positive regulation of epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / establishment of skin barrier / 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 / TP53 Regulates Metabolic Genes / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of protein kinase activity / multicellular organism growth / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of canonical Wnt signaling pathway / 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
4-methyl-5-phenyl-thiophene-2-carboximidamide / 14-3-3 protein sigma / WW domain-containing transcription regulator protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOttmann, C. / Wolter, M. / Guillory, X. / Leysen, S. / Genet, S. / Somsen, B. / Patel, J. / Castaldi, P.
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
DepositionAug 20, 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: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0664
Polymers29,6332
Non-polymers4332
Water4,864270
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)60,1318
Polymers59,2664
Non-polymers8654
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.001, 112.204, 62.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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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 WW domain-containing transcription regulator protein 1 / Transcriptional coactivator with PDZ-binding motif


Mass: 1422.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9GZV5
#3: Chemical ChemComp-L1T / 4-methyl-5-phenyl-thiophene-2-carboximidamide


Mass: 216.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
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: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2→34.03 Å / Num. obs: 19958 / % possible obs: 99.85 % / Redundancy: 2 % / Biso Wilson estimate: 12.4182991847 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04702 / Rrim(I) all: 0.06649 / Net I/σ(I): 11.54
Reflection shellResolution: 2→2.072 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1212 / Mean I/σ(I) obs: 3.85 / Num. unique obs: 1949 / CC1/2: 0.954 / Rrim(I) all: 0.1713 / % possible all: 99.24

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.12_2829refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHR

3mhr


Resolution: 2→34.03 Å / SU ML: 0.17058947998 / Cross valid method: FREE R-VALUE / σ(F): 1.50086671106 / Phase error: 21.9482538694
RfactorNum. reflection% reflection
Rfree0.215365513269 1830 4.85205217945 %
Rwork0.182679473135 --
obs0.184391893594 19956 99.5696824098 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.5842942024 Å2
Refinement stepCycle: LAST / Resolution: 2→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 30 270 2161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00995705175741975
X-RAY DIFFRACTIONf_angle_d1.017653798282672
X-RAY DIFFRACTIONf_chiral_restr0.0450596784053290
X-RAY DIFFRACTIONf_plane_restr0.00692775202479352
X-RAY DIFFRACTIONf_dihedral_angle_d16.82551088941206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.00003622115-2.05410.2304717236211240.1859338034982745X-RAY DIFFRACTION98.3207676491
2.0541-2.11450.2169950610581360.1659016226252800X-RAY DIFFRACTION99.8299897994
2.1145-2.18280.2140098639211540.1604622349012736X-RAY DIFFRACTION100
2.1828-2.26080.2168718973971270.1759118024712751X-RAY DIFFRACTION100
2.2608-2.35130.2062849928411300.1823726314492808X-RAY DIFFRACTION100
2.3513-2.45830.2577672558711190.2013460128242798X-RAY DIFFRACTION100
2.4583-2.58780.2464484179421370.2023635212622780X-RAY DIFFRACTION100
2.5878-2.74990.2951903464241570.2113899634142755X-RAY DIFFRACTION100
2.7499-2.96210.2513726186141360.2104986004462753X-RAY DIFFRACTION99.9308197855
2.9621-3.260.220035404691450.1780113935392759X-RAY DIFFRACTION99.4180075317
3.26-3.73120.1729772952961540.1542342529772732X-RAY DIFFRACTION98.8356164384
3.7312-4.69890.1812386443421720.1677233802172699X-RAY DIFFRACTION98.625901752
4.6989-34.030.2070911857481390.199522607932770X-RAY DIFFRACTION99.5210400274

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