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- PDB-9qng: FOXO3 pS413 phosphopeptide binding to 14-3-3sigma -

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Basic information

Entry
Database: PDB / ID: 9qng
TitleFOXO3 pS413 phosphopeptide binding to 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • Forkhead box protein O3
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 protein-protein interactions
Function / homology
Function and homology information


positive regulation of muscle atrophy / initiation of primordial ovarian follicle growth / positive regulation of hydrogen peroxide-mediated programmed cell death / mitochondrial transcription factor activity / RUNX3 regulates BCL2L11 (BIM) transcription / RNA polymerase II transcription repressor complex / FOXO-mediated transcription of cell cycle genes / cellular response to corticosterone stimulus / AKT phosphorylates targets in the nucleus / response to water-immersion restraint stress ...positive regulation of muscle atrophy / initiation of primordial ovarian follicle growth / positive regulation of hydrogen peroxide-mediated programmed cell death / mitochondrial transcription factor activity / RUNX3 regulates BCL2L11 (BIM) transcription / RNA polymerase II transcription repressor complex / FOXO-mediated transcription of cell cycle genes / cellular response to corticosterone stimulus / AKT phosphorylates targets in the nucleus / response to water-immersion restraint stress / neuronal stem cell population maintenance / ovulation from ovarian follicle / regulation of neural precursor cell proliferation / response to fatty acid / mitochondrial transcription / Signaling by NODAL / brain morphogenesis / Regulation of FOXO transcriptional activity by acetylation / oocyte maturation / positive regulation of regulatory T cell differentiation / antral ovarian follicle growth / response to starvation / negative regulation of neuron differentiation / response to dexamethasone / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / FOXO-mediated transcription of cell death genes / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of reactive oxygen species biosynthetic process / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / positive regulation of endothelial cell apoptotic process / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / Mitochondrial unfolded protein response (UPRmt) / canonical Wnt signaling pathway / establishment of skin barrier / negative regulation of protein localization to plasma membrane / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / extrinsic apoptotic signaling pathway in absence of ligand / FLT3 Signaling / positive regulation of autophagy / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / positive regulation of erythrocyte differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of cell migration / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / tumor necrosis factor-mediated signaling pathway / stem cell proliferation / transcription coregulator binding / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / DNA damage response, signal transduction by p53 class mediator / cellular response to glucose stimulus / negative regulation of canonical Wnt signaling pathway / MAPK6/MAPK4 signaling / cellular response to nerve growth factor stimulus / beta-catenin binding / chromatin DNA binding / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to amyloid-beta / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / intracellular protein localization / positive regulation of neuron apoptotic process / regulation of translation / regulation of protein localization / positive regulation of cell growth / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / sequence-specific DNA binding / mitochondrial outer membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of apoptotic process / cadherin binding
Similarity search - Function
FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. ...FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / 14-3-3 protein sigma / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Forkhead box protein O3 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPennings, M.A.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101077879European Union
CitationJournal: Digit Discov / Year: 2025
Title: Identifying 14-3-3 interactome binding sites with deep learning.
Authors: van Weesep, L. / Ozcelik, R. / Pennings, M. / Criscuolo, E. / Ottmann, C. / Brunsveld, L. / Grisoni, F.
History
DepositionMar 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: 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

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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
B: Forkhead box protein O3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9058
Polymers27,6692
Non-polymers2366
Water4,540252
1
A: 14-3-3 protein sigma
B: Forkhead box protein O3
hetero molecules

A: 14-3-3 protein sigma
B: Forkhead box protein O3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81016
Polymers55,3384
Non-polymers47212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5420 Å2
ΔGint-108 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.147, 112.039, 63.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

CA

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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 Forkhead box protein O3 / AF6q21 protein / Forkhead in rhabdomyosarcoma-like 1


Mass: 1126.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43524
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES pH=7.1-7.7 0.19 M CaCl2 5% glycerol 24-29% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.35→63.07 Å / Num. obs: 64111 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 1.35→1.37 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3155 / CC1/2: 0.394

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Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→45.72 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.395 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18876 3293 5.1 %RANDOM
Rwork0.16047 ---
obs0.16195 60788 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.752 Å2
Baniso -1Baniso -2Baniso -3
1-4.6 Å20 Å2-0 Å2
2---1.98 Å20 Å2
3----2.62 Å2
Refinement stepCycle: LAST / Resolution: 1.35→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 6 252 2192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0162032
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161935
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.822749
X-RAY DIFFRACTIONr_angle_other_deg0.4561.5674476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5255.301282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42210391
X-RAY DIFFRACTIONr_chiral_restr0.050.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_mcbond_it5.4622.0851000
X-RAY DIFFRACTIONr_mcbond_other5.4472.0841000
X-RAY DIFFRACTIONr_mcangle_it7.7283.7611252
X-RAY DIFFRACTIONr_mcangle_other7.7423.7651253
X-RAY DIFFRACTIONr_scbond_it7.9352.4481032
X-RAY DIFFRACTIONr_scbond_other7.9112.4471032
X-RAY DIFFRACTIONr_scangle_other11.2754.3431487
X-RAY DIFFRACTIONr_long_range_B_refined14.90426.892449
X-RAY DIFFRACTIONr_long_range_B_other13.87423.872384
X-RAY DIFFRACTIONr_rigid_bond_restr3.39433967
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 242 -
Rwork0.345 4465 -
obs--99.98 %

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