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- PDB-6g6x: 14-3-3sigma in complex with a P129beta3P mutated YAP pS127 phosph... -

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Basic information

Entry
Database: PDB / ID: 6g6x
Title14-3-3sigma in complex with a P129beta3P mutated YAP pS127 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Transcriptional coactivator YAP1
KeywordsONCOPROTEIN / beta amino acid hippo pathway YAP/TAZ
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / polarized epithelial cell differentiation / bud elongation involved in lung branching / RUNX3 regulates YAP1-mediated transcription ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / polarized epithelial cell differentiation / bud elongation involved in lung branching / RUNX3 regulates YAP1-mediated transcription / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of stem cell proliferation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of epithelial cell apoptotic process / intestinal epithelial cell development / tissue homeostasis / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / organ growth / negative regulation of epithelial cell differentiation / interleukin-6-mediated signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / regulation of cell-cell adhesion / cAMP/PKA signal transduction / regulation of neurogenesis / Regulation of localization of FOXO transcription factors / somatic stem cell population maintenance / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / bicellular tight junction / establishment of skin barrier / canonical Wnt signaling pathway / negative regulation of protein localization to plasma membrane / positive regulation of osteoblast differentiation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / vasculogenesis / Nuclear signaling by ERBB4 / negative regulation of stem cell proliferation / keratinocyte differentiation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of cardiac muscle cell proliferation / RHO GTPases activate PKNs / cellular response to retinoic acid / positive regulation of protein localization / extrinsic apoptotic signaling pathway / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / response to progesterone / positive regulation of epithelial cell proliferation / epithelial cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / transcription coregulator activity / wound healing / cellular response to gamma radiation / cell morphogenesis / positive regulation of protein localization to nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / transcription corepressor activity / cell junction / positive regulation of canonical Wnt signaling pathway / intracellular protein localization / cell-cell junction / regulation of protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly
Similarity search - Function
: / Omega loop, TEAD interating region 3 / : / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...: / Omega loop, TEAD interating region 3 / : / 14-3-3 domain / Delta-Endotoxin; domain 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsAndrei, S.A. / Thijssen, V. / Brunsveld, L. / Ottmann, C. / Milroy, L.G.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchECHO-STIP 717.014.001 Netherlands
Netherlands Organisation for Scientific ResearchGravity program 024.001.035 Netherlands
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: A study on the effect of synthetic alpha-to-beta3-amino acid mutations on the binding of phosphopeptides to 14-3-3 proteins.
Authors: Andrei, S.A. / Thijssen, V. / Brunsveld, L. / Ottmann, C. / Milroy, L.G.
History
DepositionApr 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9068
Polymers27,7182
Non-polymers1886
Water7,188399
1
A: 14-3-3 protein sigma
P: Transcriptional coactivator YAP1
hetero molecules

A: 14-3-3 protein sigma
P: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81216
Polymers55,4364
Non-polymers37612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6130 Å2
ΔGint-138 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.118, 111.849, 62.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-700-

HOH

31A-771-

HOH

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Components

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


Mass: 26542.914 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 Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 1175.190 Da / Num. of mol.: 1 / Mutation: Proline 129 to beta3-proline / Source method: obtained synthetically / Details: EOE = beta3-proline / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES, pH 7.1, 29% PEG 400, 0.19 M CaCl2, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.13→45.49 Å / Num. obs: 107708 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 10.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Net I/σ(I): 14.1 / Num. measured all: 1208392 / Scaling rejects: 9132
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.13-1.158.11.35952830.7670.5051.45599.9
6.19-45.4912.90.0727440.9930.0210.07599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.3 Å45.49 Å
Translation5.3 Å45.49 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.6.3data scaling
PHASER2.8.1phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mhr

3mhr


Resolution: 1.13→45.49 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.29
RfactorNum. reflection% reflection
Rfree0.1678 2705 2.51 %
Rwork0.1496 --
obs0.15 107651 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.71 Å2 / Biso mean: 17.7075 Å2 / Biso min: 4.11 Å2
Refinement stepCycle: final / Resolution: 1.13→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 6 399 2330
Biso mean--19.67 28.93 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.13-1.15060.35391320.407154725604
1.1506-1.17270.33771190.294955135632
1.1727-1.19660.23651230.24154895612
1.1966-1.22260.24041530.212954395592
1.2226-1.25110.20611380.186654715609
1.2511-1.28240.20471510.175254985649
1.2824-1.3170.17051360.160654855621
1.317-1.35580.18721470.152554765623
1.3558-1.39960.15241360.128754865622
1.3996-1.44960.13691390.122655065645
1.4496-1.50760.15041440.112155305674
1.5076-1.57630.14191520.112454825634
1.5763-1.65940.13671400.113854955635
1.6594-1.76330.13021370.122755305667
1.7633-1.89950.16281440.131155405684
1.8995-2.09060.14461510.128455565707
2.0906-2.39310.14531560.127655755731
2.3931-3.0150.16281570.152456045761
3.015-45.53060.18151500.162257995949

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