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- PDB-7tdw: Structure of FOXP3-DNA complex -

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Basic information

Entry
Database: PDB / ID: 7tdw
TitleStructure of FOXP3-DNA complex
Components
  • DNA (5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*AP*CP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*GP*TP*AP*AP*AP*CP*AP*AP*AP*TP*TP*T)-3')
  • Forkhead box P3
KeywordsTRANSCRIPTION/DNA / FOXP3 / Dimer / Forkhead / DNA / Treg / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


: / : / establishment of endothelial blood-brain barrier / response to rapamycin / negative regulation of interleukin-4 production / negative regulation of CREB transcription factor activity / negative regulation of T cell cytokine production / negative regulation of defense response to virus / negative regulation of T-helper 17 cell differentiation / positive regulation of regulatory T cell differentiation ...: / : / establishment of endothelial blood-brain barrier / response to rapamycin / negative regulation of interleukin-4 production / negative regulation of CREB transcription factor activity / negative regulation of T cell cytokine production / negative regulation of defense response to virus / negative regulation of T-helper 17 cell differentiation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / negative regulation of interleukin-2 production / histone acetyltransferase binding / negative regulation of interleukin-10 production / negative regulation of NF-kappaB transcription factor activity / NFAT protein binding / negative regulation of type II interferon production / negative regulation of T cell proliferation / T cell activation / response to virus / response to radiation / histone deacetylase binding / sequence-specific double-stranded DNA binding / response to lipopolysaccharide / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / cytoplasm
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. / Zinc finger C2H2-type ...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. / Zinc finger C2H2-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box P3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsLeng, F. / Hur, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Immunity / Year: 2022
Title: The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis.
Authors: Leng, F. / Zhang, W. / Ramirez, R.N. / Leon, J. / Zhong, Y. / Hou, L. / Yuki, K. / van der Veeken, J. / Rudensky, A.Y. / Benoist, C. / Hur, S.
History
DepositionJan 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Forkhead box P3
B: DNA (5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*AP*CP*TP*C)-3')
C: DNA (5'-D(P*GP*AP*GP*TP*AP*AP*AP*CP*AP*AP*AP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)30,7153
Polymers30,7153
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-21 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.092, 92.092, 179.398
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Forkhead box P3 / Scurfin


Mass: 22158.365 Da / Num. of mol.: 1 / Fragment: UNP residues 204-276,305-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Foxp3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53Z59
#2: DNA chain DNA (5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*AP*CP*TP*C)-3')


Mass: 4244.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(P*GP*AP*GP*TP*AP*AP*AP*CP*AP*AP*AP*TP*TP*T)-3')


Mass: 4311.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.59 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl, pH 8.5, 12% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4→72.88 Å / Num. obs: 4178 / % possible obs: 99.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 174.77 Å2 / CC1/2: 1 / Net I/σ(I): 7.4
Reflection shellResolution: 4→4.14 Å / Num. unique obs: 398 / CC1/2: 0.935

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6EL8

6el8


Resolution: 4→72.88 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.6994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3592 211 5.19 %
Rwork0.3347 3853 -
obs0.3358 4064 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 269.17 Å2
Refinement stepCycle: LAST / Resolution: 4→72.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 571 0 0 1349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00351448
X-RAY DIFFRACTIONf_angle_d0.58482082
X-RAY DIFFRACTIONf_chiral_restr0.0344219
X-RAY DIFFRACTIONf_plane_restr0.0043167
X-RAY DIFFRACTIONf_dihedral_angle_d31.2918375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-5.040.4936980.45881832X-RAY DIFFRACTION95.4
5.04-72.880.32511130.29752021X-RAY DIFFRACTION97.76

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