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- PDB-6g8p: 14-3-3sigma in complex with a P129beta3P and L132beta3L mutated Y... -

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Basic information

Entry
Database: PDB / ID: 6g8p
Title14-3-3sigma in complex with a P129beta3P and L132beta3L 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 / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of stem cell proliferation / 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 / regulation of epidermal cell division / protein kinase C inhibitor activity / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / positive regulation of epidermal cell differentiation / keratinocyte development / negative regulation of fat cell differentiation / keratinization / positive regulation of stem cell population maintenance / regulation of cell-cell adhesion / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / somatic stem cell population maintenance / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / regulation of neurogenesis / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / bicellular tight junction / negative regulation of protein localization to plasma membrane / canonical Wnt signaling pathway / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of osteoblast differentiation / vasculogenesis / negative regulation of stem cell proliferation / Nuclear signaling by ERBB4 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cardiac muscle cell proliferation / keratinocyte differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / protein export from nucleus / protein sequestering activity / positive regulation of cell adhesion / negative regulation of innate immune response / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / positive regulation of epithelial cell proliferation / epithelial cell proliferation / stem cell proliferation / response to progesterone / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / 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 / positive regulation of canonical Wnt signaling pathway / cell-cell junction / cell junction / protein localization / 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: 1.9 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / 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 / _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_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_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_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 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)27,8485
Polymers27,7322
Non-polymers1163
Water6,287349
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)55,69510
Polymers55,4644
Non-polymers2316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.037, 111.499, 62.460
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-731-

HOH

21A-734-

HOH

31A-736-

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: 1189.217 Da / Num. of mol.: 1 / Fragment: UNP residues 124-133 / Source method: obtained synthetically / Details: EOE and B3L are beta3-amino acid mutations / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
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: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→66.08 Å / Num. obs: 22902 / % possible obs: 99.7 % / Redundancy: 11.2 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.026 / Rrim(I) all: 0.089 / Net I/σ(I): 21.1 / Num. measured all: 257393 / Scaling rejects: 1018
Reflection shell

CC1/2: 0.983 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.948.20.1821143113990.0660.19410.395.7
9.11-66.08100.07924912490.0270.08426.199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.36 Å55.75 Å
Translation5.36 Å55.75 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.6.2data scaling
PHASER2.8.1phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mhr

3mhr


Resolution: 1.9→41.592 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.16
RfactorNum. reflection% reflection
Rfree0.1586 1181 5.17 %
Rwork0.1334 --
obs0.1348 22861 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.11 Å2 / Biso mean: 22.0283 Å2 / Biso min: 6.66 Å2
Refinement stepCycle: final / Resolution: 1.9→41.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 19 349 2256
Biso mean--17.59 32.28 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.98650.17921430.14142599274297
1.9865-2.09120.17141690.126326452814100
2.0912-2.22220.17591490.1226992848100
2.2222-2.39380.1441320.115327022834100
2.3938-2.63470.15061410.121526992840100
2.6347-3.01580.17991480.14127362884100
3.0158-3.79920.13891450.126227342879100
3.7992-41.60160.15661540.154328663020100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4856-0.1810.40341.3786-0.52951.0288-0.05690.00010.03760.00130.06090.05690.0055-0.03910.00130.0783-0.00390.00120.07640.00930.096728.8215-10.77760.5812
21.8316-0.62560.90430.2137-0.32870.94230.06770.50010.4334-0.66870.24010.6798-0.3186-0.579-0.03850.60010.0916-0.110.43210.12710.413925.504111.6251-27.8111
30.41170.02380.05492.1022-0.47020.769-0.04290.0267-0.0366-0.18630.0381-0.09740.03960.03940.00370.0763-0.0260.00080.1030.00330.08731.3424-14.8718-10.3289
42.38381.4979-1.1333.2788-2.10093.4216-0.09960.1226-0.1814-0.32210.0032-0.1690.18680.12530.03940.10870.00020.00770.1115-0.03670.099726.1721-27.0878-16.0835
51.18840.4706-0.21130.4716-0.17221.2650.0019-0.01890.0339-0.03870.04520.08530.0442-0.1159-0.0270.1112-0.0321-0.00660.1468-0.00490.137812.459-25.9129-12.2695
61.5810.1837-0.35163.8375-3.55055.5881-0.063-0.05150.11440.3180.03650.0878-0.4522-0.4255-0.04970.13080.0178-0.00120.1894-0.00870.17786.8649-20.6132-6.468
75.14331.51850.33524.0218-1.35076.855-0.10270.00270.1504-0.14140.01670.3723-0.4275-0.53030.05490.1294-0.00470.0110.1906-0.02720.208615.3041-14.3131-9.882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 70 )A-4 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 79 )A71 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 139 )A80 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 161 )A140 - 161
5X-RAY DIFFRACTION5chain 'A' and (resid 162 through 209 )A162 - 209
6X-RAY DIFFRACTION6chain 'A' and (resid 210 through 231 )A210 - 231
7X-RAY DIFFRACTION7chain 'P' and (resid 125 through 128 )P125 - 128

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