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- PDB-6qzs: 14-3-3 sigma in complex with FOXO1 pS256 peptide -

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Basic information

Entry
Database: PDB / ID: 6qzs
Title14-3-3 sigma in complex with FOXO1 pS256 peptide
Components
  • 14-3-3 protein sigma
  • FOXO1 pS256 site
KeywordsPEPTIDE BINDING PROTEIN / protein binding / complex / FOXO1 / 14-3-3
Function / homology
Function and homology information


cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / response to fatty acid / cellular response to cold / negative regulation of stress-activated MAPK cascade / protein acetylation ...cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / response to fatty acid / cellular response to cold / negative regulation of stress-activated MAPK cascade / protein acetylation / Regulation of FOXO transcriptional activity by acetylation / negative regulation of fat cell differentiation / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / FOXO-mediated transcription of cell death genes / energy homeostasis / temperature homeostasis / Constitutive Signaling by AKT1 E17K in Cancer / Regulation of gene expression in beta cells / regulation of cell-cell adhesion / establishment of skin barrier / Regulation of localization of FOXO transcription factors / Regulation of GBP-mediated host defense / negative regulation of insulin secretion / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / fat cell differentiation / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cAMP/PKA signal transduction / protein export from nucleus / positive regulation of gluconeogenesis / release of cytochrome c from mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of protein export from nucleus / cellular response to nitric oxide / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / intracellular glucose homeostasis / positive regulation of autophagy / protein phosphatase 2A binding / cellular response to starvation / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein sequestering activity / promoter-specific chromatin binding / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / beta-catenin binding / MAPK6/MAPK4 signaling / insulin receptor signaling pathway / intracellular protein localization / autophagy / positive regulation of protein catabolic process / cellular response to insulin stimulus / regulation of protein localization / positive regulation of cell growth / Interleukin-4 and Interleukin-13 signaling / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cadherin binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / DNA damage response / protein kinase binding / positive regulation of DNA-templated transcription / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / : / DNA-templated transcription / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 ...: / 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 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Forkhead box protein O1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOttmann, C. / Wolter, M. / Lau, R.A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission Netherlands
CitationJournal: J.Biol.Chem. / Year: 2019
Title: AMPK and AKT protein kinases hierarchically phosphorylate the N-terminus of the FOXO1 transcription factor, modulating interactions with 14-3-3 proteins.
Authors: Saline, M. / Badertscher, L. / Wolter, M. / Lau, R. / Gunnarsson, A. / Jacso, T. / Norris, T. / Ottmann, C. / Snijder, A.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Sep 11, 2019Group: Data collection / 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 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
Revision 1.4Oct 9, 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: FOXO1 pS256 site
B: 14-3-3 protein sigma
C: FOXO1 pS256 site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8997
Polymers59,4324
Non-polymers4673
Water10,647591
1
B: 14-3-3 protein sigma
C: FOXO1 pS256 site

A: 14-3-3 protein sigma
P: FOXO1 pS256 site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8997
Polymers59,4324
Non-polymers4673
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area4900 Å2
ΔGint-25 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.429, 104.619, 156.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 28226.518 Da / Num. of mol.: 2
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 FOXO1 pS256 site


Mass: 1489.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12778*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris propane, pH7 0.2 M Sodium citrate tribasic dihydrate 20 % w/v PEG 3350 10 % w/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→58.8 Å / Num. obs: 83148 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.113 / Net I/σ(I): 13.02
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 4011 / Rrim(I) all: 0.771 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHR

3mhr


Resolution: 1.9→58.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 --RANDOM
Rwork0.1816 ---
obs-78962 99.85 %-
Refinement stepCycle: LAST / Resolution: 1.9→58.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 31 591 4388

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