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- PDB-1e17: Solution structure of the DNA binding domain of the human Forkhea... -

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Basic information

Entry
Database: PDB / ID: 1.0E+17
TitleSolution structure of the DNA binding domain of the human Forkhead transcription factor AFX (FOXO4)
ComponentsAFX
KeywordsDNA BINDING DOMAIN / WINGED HELIX
Function / homology
Function and homology information


negative regulation of smooth muscle cell differentiation / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / response to water-immersion restraint stress / negative regulation of G0 to G1 transition / Cardiogenesis / muscle organ development / Regulation of FOXO transcriptional activity by acetylation / FOXO-mediated transcription of cell death genes / positive regulation of smooth muscle cell migration ...negative regulation of smooth muscle cell differentiation / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / response to water-immersion restraint stress / negative regulation of G0 to G1 transition / Cardiogenesis / muscle organ development / Regulation of FOXO transcriptional activity by acetylation / FOXO-mediated transcription of cell death genes / positive regulation of smooth muscle cell migration / Constitutive Signaling by AKT1 E17K in Cancer / mitotic G2 DNA damage checkpoint signaling / Regulation of localization of FOXO transcription factors / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of angiogenesis / response to nutrient levels / promoter-specific chromatin binding / stem cell differentiation / beta-catenin binding / sequence-specific double-stranded DNA binding / insulin receptor signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / response to oxidative stress / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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 O4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / SIMULATED ANNEALING IN TORSION ANGLE SPACE
AuthorsWeigelt, J. / Climent, I. / Dahlman-Wright, K. / Wikstrom, M.
CitationJournal: J.Biomol.NMR / Year: 2000
Title: 1H, 13C and 15N Resonance Assignments of the DNA Binding Domain of the Human Forkhead Transcription Factor Afx
Authors: Weigelt, J. / Climent, I. / Dahlman-Wright, K. / Wikstrom, M.
History
DepositionApr 25, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AFX


Theoretical massNumber of molelcules
Total (without water)16,6121
Polymers16,6121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 85LOWEST X-PLOR ENERGY
RepresentativeModel #1

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Components

#1: Protein AFX


Mass: 16611.670 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: NUCLEUS & CYTOPLASM / Plasmid: PET15B / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P98177
Sequence detailsGLY 58 - PRO 81 IN PDB ENTRY BELONG TO ARTIFICIAL HIS-TAG

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: EXPERIMENTAL DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.3 / Pressure: 1 atm / Temperature: 304 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING IN TORSION ANGLE SPACE / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST X-PLOR ENERGY / Conformers calculated total number: 85 / Conformers submitted total number: 20

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