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- PDB-6qzr: 14-3-3 sigma in complex with FOXO1 pT24 peptide -

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Basic information

Entry
Database: PDB / ID: 6qzr
Title14-3-3 sigma in complex with FOXO1 pT24 peptide
Components
  • 14-3-3 protein sigma
  • Forkhead box protein O1
KeywordsPEPTIDE BINDING PROTEIN / protein binding / 14-3-3 / FOXO1
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 / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / Regulation of FOXO transcriptional activity by 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 / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / Regulation of FOXO transcriptional activity by acetylation / negative regulation of stress-activated MAPK cascade / negative regulation of cardiac muscle hypertrophy in response to stress / regulation of reactive oxygen species metabolic process / cellular response to cold / protein acetylation / temperature homeostasis / regulation of epidermal cell division / protein kinase C inhibitor activity / negative regulation of fat cell differentiation / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / blood vessel development / FOXO-mediated transcription of cell death genes / Constitutive Signaling by AKT1 E17K in Cancer / fat cell differentiation / intracellular glucose homeostasis / regulation of cell-cell adhesion / Regulation of gene expression in beta cells / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / canonical Wnt signaling pathway / 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 insulin secretion / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / energy homeostasis / positive regulation of protein localization / positive regulation of autophagy / positive regulation of gluconeogenesis / positive regulation of cell adhesion / cellular response to nitric oxide / 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 / protein phosphatase 2A binding / cellular response to starvation / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / promoter-specific chromatin binding / negative regulation of canonical Wnt signaling pathway / MAPK6/MAPK4 signaling / beta-catenin binding / chromatin DNA binding / autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of protein catabolic process / intracellular protein localization / insulin receptor signaling pathway / regulation of protein localization / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of cell growth / cellular response to oxidative stress / Interleukin-4 and Interleukin-13 signaling / gene expression / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / cadherin binding / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II
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: 2.3 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 1.1Sep 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 1.2Jan 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 1.3Oct 23, 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
B: 14-3-3 protein sigma
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: 14-3-3 protein sigma
F: 14-3-3 protein sigma
H: 14-3-3 protein sigma
G: 14-3-3 protein sigma
R: Forkhead box protein O1
J: Forkhead box protein O1
M: Forkhead box protein O1
N: Forkhead box protein O1
O: Forkhead box protein O1
P: Forkhead box protein O1
T: Forkhead box protein O1
U: Forkhead box protein O1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,19927
Polymers237,42516
Non-polymers1,77411
Water12,250680
1
A: 14-3-3 protein sigma
N: Forkhead box protein O1
hetero molecules

C: 14-3-3 protein sigma
O: Forkhead box protein O1


Theoretical massNumber of molelcules
Total (without water)59,8237
Polymers59,3564
Non-polymers4673
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area4810 Å2
ΔGint-23 kcal/mol
Surface area22420 Å2
MethodPISA
2
B: 14-3-3 protein sigma
M: Forkhead box protein O1
hetero molecules

D: 14-3-3 protein sigma
P: Forkhead box protein O1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8237
Polymers59,3564
Non-polymers4673
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area4540 Å2
ΔGint-24 kcal/mol
Surface area22020 Å2
MethodPISA
3
H: 14-3-3 protein sigma
U: Forkhead box protein O1
hetero molecules

E: 14-3-3 protein sigma
J: Forkhead box protein O1


Theoretical massNumber of molelcules
Total (without water)59,8237
Polymers59,3564
Non-polymers4673
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area4970 Å2
ΔGint-25 kcal/mol
Surface area22670 Å2
MethodPISA
4
F: 14-3-3 protein sigma
R: Forkhead box protein O1
hetero molecules

G: 14-3-3 protein sigma
T: Forkhead box protein O1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7316
Polymers59,3564
Non-polymers3742
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area4510 Å2
ΔGint-24 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.205, 62.806, 154.044
Angle α, β, γ (deg.)90.00, 103.24, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 8
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 O1 / Forkhead box protein O1A / Forkhead in rhabdomyosarcoma


Mass: 1451.613 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12778
#3: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris propane pH 7, 0.2M Sodium nitrate, 28% (w/v) PEG400, 5% (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: 2.3→118.81 Å / Num. obs: 124223 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.983 / Rrim(I) all: 0.108 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 6125 / CC1/2: 0.943 / Rrim(I) all: 0.458 / % possible all: 99.7

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Processing

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

3mhr


Resolution: 2.3→118.81 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.46 / SU ML: 0.157 / Cross valid method: FREE R-VALUE / ESU R: 0.267 / ESU R Free: 0.224 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26668 6300 5.1 %RANDOM
Rwork0.2211 ---
obs0.22341 117909 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.532 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0 Å2-0.29 Å2
2---0.17 Å2-0 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→118.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14378 0 118 680 15176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01414698
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713116
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.67219832
X-RAY DIFFRACTIONr_angle_other_deg0.9961.66130634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41551858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78222.304738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.134152494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3115103
X-RAY DIFFRACTIONr_chiral_restr0.0760.21945
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022573
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7264.1217510
X-RAY DIFFRACTIONr_mcbond_other3.7254.1217509
X-RAY DIFFRACTIONr_mcangle_it5.6096.1419342
X-RAY DIFFRACTIONr_mcangle_other5.6096.1429343
X-RAY DIFFRACTIONr_scbond_it4.0064.2787188
X-RAY DIFFRACTIONr_scbond_other4.0054.2787188
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1736.33910491
X-RAY DIFFRACTIONr_long_range_B_refined8.35748.52117040
X-RAY DIFFRACTIONr_long_range_B_other8.3548.47316932
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 458 -
Rwork0.235 8616 -
obs--99.67 %

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