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- PDB-3qrf: Structure of a domain-swapped FOXP3 dimer -

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Basic information

Entry
Database: PDB / ID: 3qrf
TitleStructure of a domain-swapped FOXP3 dimer
Components
  • (human hARRE2 DNA ...) x 2
  • Forkhead box protein P3
  • Nuclear factor of activated T-cells, cytoplasmic 2
KeywordsDNA BINDING PROTEIN/DNA / Beta Barrel / Domain Swap / Forkhead Domain / Immnoglobulin Fold / Protein-DNA Complex / Double Helix / Transcription Regulation / DNA Binding / Nucleus / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


lncRNA transcription / positive regulation of peripheral T cell tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / establishment of endothelial blood-brain barrier / response to rapamycin / transcription factor AP-1 complex / negative regulation of interleukin-4 production / negative regulation of CREB transcription factor activity / negative regulation of chronic inflammatory response / transforming growth factor beta1 production ...lncRNA transcription / positive regulation of peripheral T cell tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / establishment of endothelial blood-brain barrier / response to rapamycin / transcription factor AP-1 complex / negative regulation of interleukin-4 production / negative regulation of CREB transcription factor activity / negative regulation of chronic inflammatory response / transforming growth factor beta1 production / negative regulation of vascular associated smooth muscle cell differentiation / 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 / myotube cell development / 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 / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / T cell anergy / immature T cell proliferation in thymus / calcineurin-NFAT signaling cascade / positive regulation of T cell anergy / 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 / cartilage development / myeloid cell homeostasis / positive regulation of regulatory T cell differentiation / positive regulation of myoblast fusion / negative regulation of cytokine production / negative regulation of interleukin-2 production / RUNX1 regulates transcription of genes involved in WNT signaling / negative regulation of NF-kappaB transcription factor activity / CLEC7A (Dectin-1) induces NFAT activation / negative regulation of interleukin-10 production / NFAT protein binding / histone acetyltransferase binding / negative regulation of activated T cell proliferation / positive regulation of interleukin-4 production / T cell homeostasis / negative regulation of interleukin-6 production / negative regulation of type II interferon production / B cell homeostasis / Calcineurin activates NFAT / negative regulation of tumor necrosis factor production / NF-kappaB binding / phosphatase binding / negative regulation of DNA-binding transcription factor activity / negative regulation of T cell proliferation / positive regulation of B cell proliferation / 14-3-3 protein binding / FCERI mediated Ca+2 mobilization / cellular response to calcium ion / T cell activation / B cell receptor signaling pathway / response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / sequence-specific double-stranded DNA binding / transcription corepressor activity / cell migration / T cell receptor signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / transcription regulator complex / molecular adaptor activity / 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 / response to xenobiotic stimulus / inflammatory response / DNA-binding transcription factor activity / ribonucleoprotein complex / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
: / Nuclear factor of activated T cells (NFAT) / FOXP, coiled-coil domain / : / FOXP coiled-coil domain / Rel homology domain (RHD), DNA-binding domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD ...: / Nuclear factor of activated T cells (NFAT) / FOXP, coiled-coil domain / : / FOXP coiled-coil domain / Rel homology domain (RHD), DNA-binding domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Immunoglobulin E-set / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor of activated T-cells, cytoplasmic 2 / Forkhead box protein P3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBandukwala, H.S. / Wu, Y. / Feurer, M. / Chen, Y. / Barbosa, B. / Ghosh, S. / Stroud, J.C. / Benoist, C. / Mathis, D. / Rao, A. / Chen, L.
CitationJournal: Immunity / Year: 2011
Title: Structure of a Domain-Swapped FOXP3 Dimer on DNA and Its Function in Regulatory T Cells.
Authors: Bandukwala, H.S. / Wu, Y. / Feuerer, M. / Chen, Y. / Barboza, B. / Ghosh, S. / Stroud, J.C. / Benoist, C. / Mathis, D. / Rao, A. / Chen, L.
History
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Nuclear factor of activated T-cells, cytoplasmic 2
F: Forkhead box protein P3
G: Forkhead box protein P3
C: human hARRE2 DNA (Plus Strand)
D: human hARRE2 DNA (Minus Strand)
M: Nuclear factor of activated T-cells, cytoplasmic 2
H: Forkhead box protein P3
I: Forkhead box protein P3
A: human hARRE2 DNA (Plus Strand)
B: human hARRE2 DNA (Minus Strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,60814
Polymers130,51110
Non-polymers974
Water1267
1
N: Nuclear factor of activated T-cells, cytoplasmic 2
F: Forkhead box protein P3
G: Forkhead box protein P3
C: human hARRE2 DNA (Plus Strand)
D: human hARRE2 DNA (Minus Strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3047
Polymers65,2565
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-101 kcal/mol
Surface area29440 Å2
MethodPISA
2
A: human hARRE2 DNA (Plus Strand)
B: human hARRE2 DNA (Minus Strand)

M: Nuclear factor of activated T-cells, cytoplasmic 2
H: Forkhead box protein P3
I: Forkhead box protein P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3047
Polymers65,2565
Non-polymers492
Water181
TypeNameSymmetry operationNumber
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-101 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.667, 131.234, 68.665
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules NMFGHI

#1: Protein Nuclear factor of activated T-cells, cytoplasmic 2 / NF-ATc2 / NFATc2 / NFAT pre-existing subunit / NF-ATp / T-cell transcription factor NFAT1


Mass: 32209.703 Da / Num. of mol.: 2 / Fragment: human NFAT1 DNA Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2, NFAT1, NFATP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13469
#2: Protein
Forkhead box protein P3 / Scurfin


Mass: 10082.725 Da / Num. of mol.: 4 / Fragment: human FOXP3 DNA Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXP3, IPEX, JM2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZS1

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Human hARRE2 DNA ... , 2 types, 4 molecules CADB

#3: DNA chain human hARRE2 DNA (Plus Strand)


Mass: 6491.230 Da / Num. of mol.: 2 / Fragment: human IL-2 promoter ARRE2 site (plus strand) / Source method: obtained synthetically / Details: The core hARRE2 site occurs naturally in humans.
#4: DNA chain human hARRE2 DNA (Minus Strand)


Mass: 6389.186 Da / Num. of mol.: 2 / Fragment: human IL-2 promoter ARRE2 site (minus strand) / Source method: obtained synthetically / Details: The core hARRE2 site occurs naturally in humans.

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Non-polymers , 2 types, 11 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.63
Details: 5 mM HEPES, pH 7.63, 2 mM dithiothreitol (DTT), 0.5 mM EDTA, and 150 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 36536 / Num. obs: 35150 / % possible obs: 96.2 % / Observed criterion σ(F): 0
Reflection shellResolution: 2.8→2.93 Å / Rmerge(I) obs: 1.021 / Mean I/σ(I) obs: 4.15 / Num. unique all: 4468 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a02 - NFAT + DNA only

1a02


Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2828 3413 Random
Rwork0.2478 --
all-36536 -
obs-35150 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 1710 4 7 9105

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