+Open data
-Basic information
Entry | Database: PDB / ID: 7tdx | ||||||
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Title | Structure of FOXP3-DNA complex | ||||||
Components |
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Keywords | TRANSCRIPTION/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 | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Leng, F. / Hur, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tdx.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tdx.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 7tdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tdx_validation.pdf.gz | 431.3 KB | Display | wwPDB validaton report |
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Full document | 7tdx_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 7tdx_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 7tdx_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/7tdx ftp://data.pdbj.org/pub/pdb/validation_reports/td/7tdx | HTTPS FTP |
-Related structure data
Related structure data | 7tdwC 6el8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4244.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) |
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#2: DNA chain | Mass: 4311.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) |
#3: Protein | Mass: 20918.869 Da / Num. of mol.: 1 / Fragment: UNP residues 204-277,316-417 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.34 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / Details: 0.5 M lithium sulfate, 2% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→77.4 Å / Num. obs: 8070 / % possible obs: 99.7 % / Redundancy: 19 % / Biso Wilson estimate: 97.74 Å2 / CC1/2: 0.994 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 3.1→3.21 Å / Num. unique obs: 776 / CC1/2: 0.996 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6EL8 Resolution: 3.1→46.77 Å / SU ML: 0.2617 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 45.4104 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 137.99 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→46.77 Å
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Refine LS restraints |
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LS refinement shell |
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