[English] 日本語
Yorodumi
- PDB-6qzr: 14-3-3 sigma in complex with FOXO1 pT24 peptide -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of stress-activated MAPK cascade ...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 / negative regulation of stress-activated MAPK cascade / regulation of reactive oxygen species metabolic process / Regulation of FOXO transcriptional activity by acetylation / negative regulation of cardiac muscle hypertrophy in response to stress / cellular response to cold / FOXO-mediated transcription of cell death genes / temperature homeostasis / negative regulation of fat cell differentiation / protein acetylation / regulation of epidermal cell division / protein kinase C inhibitor activity / fat cell differentiation / positive regulation of epidermal cell differentiation / keratinocyte development / blood vessel development / keratinization / Constitutive Signaling by AKT1 E17K in Cancer / intracellular glucose homeostasis / Regulation of gene expression in beta cells / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of insulin secretion / Activation of BAD and translocation to mitochondria / cellular response to nitric oxide / negative regulation of keratinocyte proliferation / canonical Wnt signaling pathway / establishment of skin barrier / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of autophagy / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / energy homeostasis / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of gluconeogenesis / protein kinase A signaling / cellular response to starvation / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / protein phosphatase 2A binding / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / promoter-specific chromatin binding / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / beta-catenin binding / autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to insulin stimulus / positive regulation of protein catabolic process / intrinsic apoptotic signaling pathway in response to DNA damage / insulin receptor signaling pathway / cellular response to oxidative stress / gene expression / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / 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 / DNA damage response / ubiquitin protein ligase binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular exosome
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Bis-tris propane


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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more