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Basic information

Entry
Database: PDB / ID: 2kiu
TitleSolution structure and backbone dynamics of the DNA-binding domain of FOXP1: Insight into its domain swapping
ComponentsForkhead box protein P1
KeywordsDNA BINDING PROTEIN / Solution structure of the monomeric FOXP1 / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


regulation of macrophage colony-stimulating factor production / interleukin-21 production / regulation of monocyte differentiation / regulation of defense response to bacterium / regulation of chemokine (C-X-C motif) ligand 2 production / monocyte activation / positive regulation of B cell receptor signaling pathway / T follicular helper cell differentiation / regulation of interleukin-1 beta production / regulation of endothelial tube morphogenesis ...regulation of macrophage colony-stimulating factor production / interleukin-21 production / regulation of monocyte differentiation / regulation of defense response to bacterium / regulation of chemokine (C-X-C motif) ligand 2 production / monocyte activation / positive regulation of B cell receptor signaling pathway / T follicular helper cell differentiation / regulation of interleukin-1 beta production / regulation of endothelial tube morphogenesis / negative regulation of androgen receptor signaling pathway / Transcriptional regulation of pluripotent stem cells / chromatin => GO:0000785 / macrophage activation / regulation of tumor necrosis factor production / regulation of interleukin-12 production / negative regulation of B cell apoptotic process / endothelial cell activation / osteoclast development / nuclear androgen receptor binding / somatic stem cell population maintenance / core promoter sequence-specific DNA binding / positive regulation of endothelial cell migration / osteoclast differentiation / positive regulation of smooth muscle cell proliferation / : / sequence-specific double-stranded DNA binding / regulation of inflammatory response / regulation of gene expression / response to lipopolysaccharide / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA damage response / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
FOXP, coiled-coil domain / FOXP coiled-coil domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Zinc finger C2H2 type domain signature. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...FOXP, coiled-coil domain / FOXP coiled-coil domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Zinc finger C2H2 type domain signature. / 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 P1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsChuang, W. / Chu, Y.
CitationJournal: Protein Sci. / Year: 2011
Title: Solution structure and backbone dynamics of the DNA-binding domain of FOXP1: Insight into its domain swapping and DNA binding.
Authors: Chu, Y.P. / Chang, C.H. / Shiu, J.H. / Chang, Y.T. / Chen, C.Y. / Chuang, W.J.
History
DepositionMay 11, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Forkhead box protein P1


Theoretical massNumber of molelcules
Total (without water)10,5441
Polymers10,5441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Forkhead box protein P1 / FOXP1


Mass: 10544.104 Da / Num. of mol.: 1 / Fragment: DNA binding domain (UNP residues 462-548) / Mutation: A39P, C61Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 3p14.1, FOXP1, HSPC215 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H334

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the forkhead DNA-binding domain of FOXP1 A39P/C61Y mutant
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1412D 1H-15N HSQC
1513D CBCA(CO)NH
1613D HNCA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D (H)CCH-TOCSY
11013D C(CO)NH

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Sample preparation

DetailsContents: 0.7-2.5 mM [U-99% 13C; U-99% 15N] The DNA-binding domain of FOXP1-1, 20 mM phosphate buffer, 50 mM NaCl, 25 mM MgCl2, 50 mM Arg+Glu
Solvent system: 20 mM phosphate buffer, 50 mM NaCl, 25 mM MgCl2, 50 mM Arg+Glu
SampleUnits: mM / Component: The DNA-binding domain of FOXP1-1 / Isotopic labeling: [U-99% 13C; U-99% 15N] / Conc. range: 0.7-2.5
Sample conditionsIonic strength: 0.245 / pH: 5.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.185 / Developer: Brunger / Classification: refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures were calculated using a total of 1323 restraints, includng 1248 noe-derived distance constraints, 75 dihedral angle restraints, 34 hydrogen bond distance restraints, X-plor
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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