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Yorodumi- PDB-2as5: Structure of the DNA binding domains of NFAT and FOXP2 bound spec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2as5 | ||||||
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Title | Structure of the DNA binding domains of NFAT and FOXP2 bound specifically to DNA. | ||||||
Components |
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Keywords | Transcription/DNA / Forkhead Domain / RHR Domain / Rel Homology Region / IG Fold / Winged Helix-Turn-Helix / B-DNA / Transcription-DNA COMPLEX | ||||||
Function / homology | Function and homology information caudate nucleus development / putamen development / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / myotube cell development / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / calcineurin-NFAT signaling cascade / cartilage development / CLEC7A (Dectin-1) induces NFAT activation / positive regulation of myoblast fusion ...caudate nucleus development / putamen development / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / myotube cell development / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / calcineurin-NFAT signaling cascade / cartilage development / CLEC7A (Dectin-1) induces NFAT activation / positive regulation of myoblast fusion / Calcineurin activates NFAT / phosphatase binding / positive regulation of B cell proliferation / 14-3-3 protein binding / cellular response to calcium ion / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / cerebral cortex development / sequence-specific double-stranded DNA binding / cell migration / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Wu, Y. / Stroud, J.C. / Borde, M. / Bates, D.L. / Guo, L. / Han, A. / Rao, A. / Chen, L. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: FOXP3 Controls Regulatory T Cell Function through Cooperation with NFAT. Authors: Wu, Y. / Borde, M. / Heissmeyer, V. / Feuerer, M. / Lapan, A.D. / Stroud, J.C. / Bates, D.L. / Guo, L. / Han, A. / Ziegler, S.F. / Mathis, D. / Benoist, C. / Chen, L. / Rao, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2as5.cif.gz | 211.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2as5.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 2as5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2as5_validation.pdf.gz | 484.3 KB | Display | wwPDB validaton report |
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Full document | 2as5_full_validation.pdf.gz | 526.3 KB | Display | |
Data in XML | 2as5_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 2as5_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/2as5 ftp://data.pdbj.org/pub/pdb/validation_reports/as/2as5 | HTTPS FTP |
-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
-DNA chain , 2 types, 4 molecules ACBD
#1: DNA chain | Mass: 6491.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid phase synthesis #2: DNA chain | Mass: 6389.186 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 2 types, 4 molecules NMFG
#3: Protein | Mass: 32582.117 Da / Num. of mol.: 2 / Fragment: NFAT1 DNA BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2, NFAT1, NFATP / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q13469 #4: Protein | Mass: 11025.630 Da / Num. of mol.: 2 / Fragment: FOXP2 DNA BINDING DOMAIN / Mutation: D502I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FOXP2 / Plasmid: pET-30 LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O15409 |
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-Non-polymers , 2 types, 117 molecules
#5: Chemical | #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: 2.9 Å3/Da / Density % sol: 57.58 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: Cacodylic Acid, PEG 4k, Sodium Chloride, Magnesium Chloride, Glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.107 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 22, 2003 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.107 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 32927 / Num. obs: 31620 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1a02, chain N Resolution: 2.7→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Data was collected to 39.3 Angstroms. Resolutions lower than 30 was not included for refinement
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Refine analyze | Luzzati coordinate error obs: 0.45 Å / Luzzati sigma a obs: 0.6 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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