+Open data
-Basic information
Entry | Database: PDB / ID: 3qrf | ||||||
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Title | Structure of a domain-swapped FOXP3 dimer | ||||||
Components |
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Keywords | DNA 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 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 / tolerance induction to self antigen / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation ...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 / tolerance induction to self antigen / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / negative regulation of T cell cytokine production / transforming growth factor beta1 production / regulatory T cell differentiation / negative regulation of interleukin-5 production / regulation of isotype switching to IgG isotypes / negative regulation of defense response to virus / positive regulation of transforming growth factor beta1 production / negative regulation of chronic inflammatory response / T cell anergy / positive regulation of T cell anergy / T cell mediated immunity / myotube cell development / immature T cell proliferation in thymus / negative regulation of T-helper 17 cell differentiation / negative regulation of isotype switching to IgE isotypes / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / CD4-positive, alpha-beta T cell proliferation / isotype switching to IgE isotypes / calcineurin-NFAT signaling cascade / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of immature T cell proliferation in thymus / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of immune response / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / regulation of T cell anergy / cartilage development / negative regulation of cytokine production / myeloid cell homeostasis / negative regulation of interleukin-2 production / histone acetyltransferase binding / CLEC7A (Dectin-1) induces NFAT activation / negative regulation of interleukin-10 production / RUNX1 regulates transcription of genes involved in WNT signaling / positive regulation of myoblast fusion / negative regulation of NF-kappaB transcription factor activity / NFAT protein binding / T cell homeostasis / negative regulation of activated T cell proliferation / negative regulation of interleukin-6 production / B cell homeostasis / negative regulation of type II interferon production / Calcineurin activates NFAT / negative regulation of tumor necrosis factor production / NF-kappaB binding / positive regulation of interleukin-4 production / phosphatase binding / positive regulation of B cell proliferation / negative regulation of T cell proliferation / cellular response to calcium ion / T cell activation / FCERI mediated Ca+2 mobilization / 14-3-3 protein binding / B cell receptor signaling pathway / response to virus / negative regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / transcription corepressor activity / cell migration / sequence-specific double-stranded DNA binding / T cell receptor signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / response to lipopolysaccharide / transcription by RNA polymerase II / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / response to xenobiotic stimulus / inflammatory response / ribonucleoprotein complex / 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 / DNA damage response / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Bandukwala, H.S. / Wu, Y. / Feurer, M. / Chen, Y. / Barbosa, B. / Ghosh, S. / Stroud, J.C. / Benoist, C. / Mathis, D. / Rao, A. / Chen, L. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qrf.cif.gz | 239 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qrf.ent.gz | 186.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/3qrf ftp://data.pdbj.org/pub/pdb/validation_reports/qr/3qrf | HTTPS FTP |
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-Related structure data
Related structure data | 1a02S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules NMFGHI
#1: Protein | 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 | 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 | 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 | 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 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.42 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97625 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 36536 / Num. obs: 35150 / % possible obs: 96.2 % / Observed criterion σ(F): 0 |
Reflection shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1a02 - NFAT + DNA only Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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