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- PDB-6qvw: Solution structure of the free FOXO1 DNA binding domain -

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Basic information

Entry
Database: PDB / ID: 6qvw
TitleSolution structure of the free FOXO1 DNA binding domain
ComponentsForkhead box protein O1
KeywordsTRANSCRIPTION / FOXO1 / trasncription factor / DNA binding
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 / regulation of neural precursor cell proliferation / neuronal stem cell population maintenance / 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 / regulation of neural precursor cell proliferation / neuronal stem cell population maintenance / response to fatty acid / negative regulation of stress-activated MAPK cascade / Regulation of FOXO transcriptional activity by acetylation / negative regulation of cardiac muscle hypertrophy in response to stress / regulation of reactive oxygen species metabolic process / cellular response to cold / FOXO-mediated transcription of cell death genes / temperature homeostasis / protein acetylation / negative regulation of fat cell differentiation / blood vessel development / fat cell differentiation / intracellular glucose homeostasis / Constitutive Signaling by AKT1 E17K in Cancer / Regulation of gene expression in beta cells / Regulation of localization of FOXO transcription factors / cellular response to nitric oxide / canonical Wnt signaling pathway / negative regulation of insulin secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of autophagy / energy homeostasis / positive regulation of gluconeogenesis / cellular response to starvation / protein phosphatase 2A binding / promoter-specific chromatin binding / MAPK6/MAPK4 signaling / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / beta-catenin binding / cellular response to insulin stimulus / autophagy / positive regulation of protein catabolic process / insulin receptor signaling pathway / cellular response to oxidative stress / gene expression / 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 / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / ubiquitin protein ligase binding / chromatin / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / 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. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Forkhead box protein O1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsPsenakova, K. / Obsil, T. / Veverka, V. / Obsilova, V. / Kohoutova, K.
CitationJournal: Cells / Year: 2019
Title: Forkhead Domains of FOXO Transcription Factors Differ in both Overall Conformation and Dynamics.
Authors: Psenakova, K. / Kohoutova, K. / Obsilova, V. / Ausserlechner, M.J. / Veverka, V. / Obsil, T.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Forkhead box protein O1


Theoretical massNumber of molelcules
Total (without water)13,2151
Polymers13,2151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10180 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Forkhead box protein O1 / Forkhead box protein O1A / Forkhead in rhabdomyosarcoma


Mass: 13214.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXO1, FKHR, FOXO1A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q12778

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D CBCA(CO)NH
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY
171isotropic23D N-edited NOESY
181isotropic23D C-edited NOESY

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Sample preparation

DetailsType: solution
Contents: 380 uM [U-13C; U-15N] FOXO1 DBD, 20 mM sodium phosphate, 50 mM potassium chloride, 2 mM TCEP, 100 % n/a n/a, 90% H2O/10% D2O
Label: CN / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
380 uMFOXO1 DBD[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
50 mMpotassium chloridenatural abundance1
2 mMTCEPnatural abundance1
Sample conditionsIonic strength: 70 mM / Label: c1 / pH: 6.5 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddard, NMRFAMchemical shift assignment
YASARAYASARArefinement
TopSpinBruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 30

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