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- PDB-4wk8: FOXP3 forms a domain-swapped dimer to bridge DNA -

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Basic information

Entry
Database: PDB / ID: 4wk8
TitleFOXP3 forms a domain-swapped dimer to bridge DNA
Components
  • DNA (5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3')
  • DNA (5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3')
  • Forkhead box protein P3
KeywordsTRANSCRIPTION/DNA / FOXP3 / regulatory T cells / DNA bridging / transcription regulation / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


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 / 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 T cell cytokine production / negative regulation of interleukin-5 production ...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 / 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 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 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 / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / 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 / positive regulation of regulatory T cell differentiation / negative regulation of cytokine production / myeloid cell homeostasis / negative regulation of interleukin-2 production / RUNX1 regulates transcription of genes involved in WNT signaling / negative regulation of interleukin-10 production / histone acetyltransferase binding / NFAT protein binding / positive regulation of interleukin-4 production / negative regulation of NF-kappaB transcription factor activity / negative regulation of activated T cell proliferation / T cell homeostasis / negative regulation of interleukin-6 production / B cell homeostasis / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / NF-kappaB binding / negative regulation of T cell proliferation / T cell activation / negative regulation of DNA-binding transcription factor activity / response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / transcription corepressor activity / sequence-specific double-stranded DNA binding / T cell receptor signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / 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 / nucleus / cytosol / 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. ...: / 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-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
DNA / DNA (> 10) / Forkhead box protein P3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4006 Å
AuthorsChen, Y. / Chen, L.
Funding support United States, China, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM064642 United States
National Natural Science Foundation of China (NSFC)81372904 China
National Natural Science Foundation of China (NSFC)81272971 China
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.
Authors: Chen, Y. / Chen, C. / Zhang, Z. / Liu, C.C. / Johnson, M.E. / Espinoza, C.A. / Edsall, L.E. / Ren, B. / Zhou, X.J. / Grant, S.F. / Wells, A.D. / Chen, L.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,0464
Polymers33,0464
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-79 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.431, 84.837, 68.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain DNA (5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3')


Mass: 6491.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3')


Mass: 6389.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Forkhead box protein P3 / Scurfin


Mass: 10082.725 Da / Num. of mol.: 2 / Fragment: UNP residues 336-417
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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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: 65.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 8000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 7159 / % possible obs: 93.9 % / Redundancy: 5.4 % / Net I/σ(I): 10.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 3.4006→44.541 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 649 9.94 %
Rwork0.1903 --
obs0.1964 6529 94.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4006→44.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 855 0 0 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142394
X-RAY DIFFRACTIONf_angle_d1.5693419
X-RAY DIFFRACTIONf_dihedral_angle_d29.11934
X-RAY DIFFRACTIONf_chiral_restr0.066364
X-RAY DIFFRACTIONf_plane_restr0.008284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4006-3.66310.29561010.2441964X-RAY DIFFRACTION80
3.6631-4.03150.32741280.21511157X-RAY DIFFRACTION95
4.0315-4.61430.24641360.19241214X-RAY DIFFRACTION99
4.6143-5.81150.21981390.18421233X-RAY DIFFRACTION100
5.8115-44.5450.22851450.16211312X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -20.2487 Å / Origin y: 1.1245 Å / Origin z: -7.3154 Å
111213212223313233
T0.1465 Å2-0.0299 Å2-0.0543 Å2-0.2284 Å2-0.0192 Å2--0.1414 Å2
L0.3595 °2-0.5033 °20.2905 °2-2.8337 °2-1.2199 °2--1.3524 °2
S0.1827 Å °0.0818 Å °0.0317 Å °-0.1924 Å °-0.1249 Å °-0.0799 Å °-0.0872 Å °-0.1743 Å °0.0527 Å °
Refinement TLS groupSelection details: all

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