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- PDB-9d2l: FoxP3 multimers bridge four T2G repeat DNAs -

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Basic information

Entry
Database: PDB / ID: 9d2l
TitleFoxP3 multimers bridge four T2G repeat DNAs
Components
  • DNA (47-MER)
  • DNA (48-MER)
  • Forkhead box protein P3
KeywordsTRANSCRIPTION/DNA / FoxP3 / STRs / transcriptional factor / FKH / DNA bridging / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


T cell tolerance induction / positive regulation of peripheral T cell tolerance induction / tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / establishment of endothelial blood-brain barrier / positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of alpha-beta T cell proliferation / response to rapamycin / alpha-beta T cell proliferation / negative regulation of interleukin-4 production ...T cell tolerance induction / positive regulation of peripheral T cell tolerance induction / tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / establishment of endothelial blood-brain barrier / positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of alpha-beta T cell proliferation / response to rapamycin / alpha-beta T cell proliferation / negative regulation of interleukin-4 production / negative regulation of CREB transcription factor activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / negative regulation of chronic inflammatory response / transforming growth factor beta1 production / negative regulation of T cell cytokine production / negative regulation of interleukin-5 production / regulation of isotype switching to IgG isotypes / regulatory T cell differentiation / tolerance induction to self antigen / negative regulation of defense response to virus / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / T cell mediated immunity / positive regulation of transforming growth factor beta1 production / negative regulation of immune response / T cell anergy / immature T cell proliferation in thymus / positive regulation of T cell tolerance induction / lymphocyte proliferation / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of immature T cell proliferation in thymus / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / negative regulation of interleukin-17 production / regulation of T cell anergy / regulation of immunoglobulin production / myeloid cell homeostasis / positive regulation of regulatory T cell differentiation / negative regulation of cytokine production / negative regulation of interleukin-2 production / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-10 production / NFAT protein binding / histone acetyltransferase binding / positive regulation of interleukin-4 production / negative regulation of interleukin-6 production / negative regulation of type II interferon production / B cell homeostasis / negative regulation of tumor necrosis factor production / T cell proliferation / negative regulation of DNA-binding transcription factor activity / negative regulation of T cell proliferation / T cell activation / negative regulation of inflammatory response / response to virus / histone deacetylase binding / transcription corepressor activity / T cell receptor signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / gene expression / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / inflammatory response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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. ...: / 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 protein P3
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLeng, F. / Hur, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: FoxP3 multimers bridge three T4G repeat DNAs
Authors: Leng, F. / Hur, S.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Forkhead box protein P3
U: Forkhead box protein P3
V: Forkhead box protein P3
F: Forkhead box protein P3
E: Forkhead box protein P3
y: Forkhead box protein P3
Z: Forkhead box protein P3
z: Forkhead box protein P3
A: Forkhead box protein P3
b: DNA (48-MER)
X: Forkhead box protein P3
W: Forkhead box protein P3
R: Forkhead box protein P3
Y: Forkhead box protein P3
g: DNA (47-MER)
d: DNA (48-MER)
c: DNA (47-MER)
K: Forkhead box protein P3
J: Forkhead box protein P3
H: Forkhead box protein P3
D: Forkhead box protein P3
B: Forkhead box protein P3
e: DNA (47-MER)
M: Forkhead box protein P3
N: Forkhead box protein P3
S: Forkhead box protein P3
O: Forkhead box protein P3
Q: Forkhead box protein P3
C: Forkhead box protein P3
P: Forkhead box protein P3
T: Forkhead box protein P3
L: Forkhead box protein P3
G: Forkhead box protein P3
h: DNA (48-MER)
f: DNA (48-MER)
a: DNA (47-MER)


Theoretical massNumber of molelcules
Total (without water)941,44936
Polymers941,44936
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Forkhead box protein P3 / Scurfin


Mass: 27282.246 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Foxp3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99JB6
#2: DNA chain
DNA (48-MER)


Mass: 21929.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (47-MER)


Mass: 22457.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FoxP3-T4G repeats complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1340131 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 22.04 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003526105
ELECTRON MICROSCOPYf_angle_d0.586837402
ELECTRON MICROSCOPYf_chiral_restr0.0354275
ELECTRON MICROSCOPYf_plane_restr0.00323494
ELECTRON MICROSCOPYf_dihedral_angle_d27.46926994

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