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- PDB-6g8k: 14-3-3sigma in complex with a S131beta3S mutated YAP pS127 phosph... -

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Basic information

Entry
Database: PDB / ID: 6g8k
Title14-3-3sigma in complex with a S131beta3S mutated YAP pS127 phosphopeptide
Components
  • 14-3-3 protein sigma
  • ACE-ARG-ALA-HIS-SEP-SER-PRO-ALA-BSE-LEU-GLN
KeywordsONCOPROTEIN / beta amino acid / hippo pathway / YAP/TAZ
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / glandular epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / bud elongation involved in lung branching / polarized epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription ...enterocyte differentiation / regulation of keratinocyte proliferation / glandular epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / bud elongation involved in lung branching / polarized epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of stem cell proliferation / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / EGR2 and SOX10-mediated initiation of Schwann cell myelination / tissue homeostasis / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / Signaling by Hippo / proline-rich region binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / organ growth / interleukin-6-mediated signaling pathway / negative regulation of epithelial cell differentiation / regulation of epidermal cell division / negative regulation of fat cell differentiation / protein kinase C inhibitor activity / positive regulation of Notch signaling pathway / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / regulation of cell-cell adhesion / positive regulation of stem cell population maintenance / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / somatic stem cell population maintenance / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / bicellular tight junction / canonical Wnt signaling pathway / negative regulation of keratinocyte proliferation / regulation of neurogenesis / establishment of skin barrier / negative regulation of protein localization to plasma membrane / positive regulation of osteoblast differentiation / vasculogenesis / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / positive regulation of cardiac muscle cell proliferation / keratinocyte differentiation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / response to progesterone / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of protein export from nucleus / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / wound healing / cellular response to gamma radiation / positive regulation of protein localization to nucleus / cell morphogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / cell-cell junction / cell junction / transcription corepressor activity / intracellular protein localization / positive regulation of canonical Wnt signaling pathway / 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 interacting 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 interacting 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: 1.25 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 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 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 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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.pdbx_ptnr2_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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: ACE-ARG-ALA-HIS-SEP-SER-PRO-ALA-BSE-LEU-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8366
Polymers27,7182
Non-polymers1184
Water6,972387
1
A: 14-3-3 protein sigma
P: ACE-ARG-ALA-HIS-SEP-SER-PRO-ALA-BSE-LEU-GLN
hetero molecules

A: 14-3-3 protein sigma
P: ACE-ARG-ALA-HIS-SEP-SER-PRO-ALA-BSE-LEU-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,67312
Polymers55,4364
Non-polymers2368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4710 Å2
ΔGint-93 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.260, 111.730, 62.510
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-416-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#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 ACE-ARG-ALA-HIS-SEP-SER-PRO-ALA-BSE-LEU-GLN


Mass: 1175.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BSE is a beta3-serine unnatural amino acid / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937*PLUS

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Non-polymers , 4 types, 391 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.53 %
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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.25→66.24 Å / Num. obs: 79674 / % possible obs: 99.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.03 / Rrim(I) all: 0.106 / Net I/σ(I): 12.4 / Num. measured all: 932846 / Scaling rejects: 435
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.25-1.277.60.85338400.6690.3240.91598.8
6.85-66.2412.70.0775620.980.0230.08199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.3 Å66.24 Å
Translation5.3 Å66.24 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: 1.25→55.865 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.08
RfactorNum. reflection% reflection
Rfree0.1597 1990 2.5 %
Rwork0.141 --
obs0.1415 79638 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.82 Å2 / Biso mean: 17.6523 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: final / Resolution: 1.25→55.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 4 387 2286
Biso mean--20.91 29.39 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.28130.25181380.2375447558599
1.2813-1.31590.25681560.254645620100
1.3159-1.35460.2191410.188155025643100
1.3546-1.39840.22581420.178455025644100
1.3984-1.44830.16971300.151355175647100
1.4483-1.50630.15441490.122255355684100
1.5063-1.57490.13381390.113254885627100
1.5749-1.65790.15311500.115355075657100
1.6579-1.76180.16821290.119655515680100
1.7618-1.89790.12971330.121755385671100
1.8979-2.08880.1341360.122455785714100
2.0888-2.39110.1421540.117755855739100
2.3911-3.01250.15531510.141556195770100
3.0125-55.92080.1641420.158658155957100

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