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- PDB-2k86: Solution Structure of FOXO3a Forkhead domain -

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Basic information

Entry
Database: PDB / ID: 2k86
TitleSolution Structure of FOXO3a Forkhead domain
ComponentsForkhead box protein O3FOX proteins
KeywordsDNA BINDING PROTEIN / Forkhead / Winged-helix / DNA binding domain / Activator / Apoptosis / Chromosomal rearrangement / Cytoplasm / DNA-binding / Nucleus / Phosphoprotein / Proto-oncogene / Transcription / Transcription regulation
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 / RNA polymerase II transcription repressor complex / mitochondrial transcription factor activity / RUNX3 regulates BCL2L11 (BIM) transcription / cellular response to corticosterone stimulus / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / ovulation from ovarian follicle ...positive regulation of muscle atrophy / initiation of primordial ovarian follicle growth / positive regulation of hydrogen peroxide-mediated programmed cell death / RNA polymerase II transcription repressor complex / mitochondrial transcription factor activity / RUNX3 regulates BCL2L11 (BIM) transcription / cellular response to corticosterone stimulus / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / ovulation from ovarian follicle / response to water-immersion restraint stress / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / mitochondrial transcription / response to fatty acid / oocyte maturation / positive regulation of regulatory T cell differentiation / Signaling by NODAL / brain morphogenesis / positive regulation of endothelial cell apoptotic process / Regulation of FOXO transcriptional activity by acetylation / positive regulation of reactive oxygen species biosynthetic process / FOXO-mediated transcription of cell death genes / antral ovarian follicle growth / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / response to dexamethasone / response to starvation / Constitutive Signaling by AKT1 E17K in Cancer / Regulation of localization of FOXO transcription factors / DNA damage response, signal transduction by p53 class mediator / negative regulation of neuron differentiation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / canonical Wnt signaling pathway / cellular response to glucose starvation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of autophagy / extrinsic apoptotic signaling pathway in absence of ligand / tumor necrosis factor-mediated signaling pathway / FLT3 Signaling / cellular response to nerve growth factor stimulus / negative regulation of cell migration / positive regulation of erythrocyte differentiation / transcription coregulator binding / cellular response to glucose stimulus / negative regulation of canonical Wnt signaling pathway / MAPK6/MAPK4 signaling / chromatin DNA binding / beta-catenin binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / regulation of translation / cellular response to oxidative stress / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / 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 / 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. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Forkhead box protein O3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, F. / Marshall, C.B. / Li, G. / Plevin, M.J. / Ikura, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Biochemical and structural characterization of an intramolecular interaction in FOXO3a and its binding with p53.
Authors: Wang, F. / Marshall, C.B. / Yamamoto, K. / Li, G.Y. / Plevin, M.J. / You, H. / Mak, T.W. / Ikura, M.
History
DepositionSep 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Forkhead box protein O3


Theoretical massNumber of molelcules
Total (without water)11,7061
Polymers11,7061
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Forkhead box protein O3 / FOX proteins / Forkhead in rhabdomyosarcoma-like 1 / AF6q21 protein


Mass: 11706.142 Da / Num. of mol.: 1 / Fragment: Forkheead (FH) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXO3, FKHRL1, FOXO3A / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43524

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D C(CO)NH
1613D H(CCO)NH
1713D 1H-15N NOESY
1823D 1H-13C NOESY
1922D 1H-13C HSQC
11023D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 50 mM potassium chloride, 2 mM DTT, 0.5 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
220 mM sodium phosphate, 50 mM potassium chloride, 2 mM DTT, 0.5 mM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate1
50 mMpotassium chloride1
2 mMDTT1
0.5 mMsodium azide1
20 mMsodium phosphate2
50 mMpotassium chloride2
2 mMDTT2
0.5 mMsodium azide2
Sample conditionsIonic strength: 0.08 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, A.T. et al.refinement
CYANAGuntert, P. et al.data analysis
NMRPipeDelaglio, F. et al.processing
XEASYBartels, C. et al.chemical shift assignment
XEASYBartels, C. et al.peak picking
TALOSCornilescu, G. et al.data analysis
ProcheckNMRLaskowski, R. et al.data analysis
NMRViewJohnson, B. et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: water refinement 'Aart J. Nederveen, Jurgen F. Doreleijers, Wim Vranken, Zachary Miller, Chris A.E.M. Spronk, Sander B. Nabuurs, Peter Guentert, Miron Livny, John L. Markley, Michael Nilges, ...Details: water refinement 'Aart J. Nederveen, Jurgen F. Doreleijers, Wim Vranken, Zachary Miller, Chris A.E.M. Spronk, Sander B. Nabuurs, Peter Guentert, Miron Livny, John L. Markley, Michael Nilges, Eldon L. Ulrich, Robert Kaptein and Alexandre M.J.J. Bonvin (2005). RECOORD: a REcalculated COORdinates Database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59, 662-672.'
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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