+Open data
-Basic information
Entry | Database: PDB / ID: 6dfs | ||||||
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Title | mouse TCR I.29 in complex with IAg7-p8E9E6ss | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T cell receptor / type 1 diabetes / autoimmunity | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å | ||||||
Authors | Wang, Y. / Dai, S. | ||||||
Citation | Journal: Sci Immunol / Year: 2019 Title: How C-terminal additions to insulin B-chain fragments create superagonists for T cells in mouse and human type 1 diabetes. Authors: Wang, Y. / Sosinowski, T. / Novikov, A. / Crawford, F. / White, J. / Jin, N. / Liu, Z. / Zou, J. / Neau, D. / Davidson, H.W. / Nakayama, M. / Kwok, W.W. / Gapin, L. / Marrack, P. / Kappler, J.W. / Dai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dfs.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dfs.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dfs_validation.pdf.gz | 486.3 KB | Display | wwPDB validaton report |
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Full document | 6dfs_full_validation.pdf.gz | 512.5 KB | Display | |
Data in XML | 6dfs_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 6dfs_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/6dfs ftp://data.pdbj.org/pub/pdb/validation_reports/df/6dfs | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 23361.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG |
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#2: Protein | Mass: 27747.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG |
#3: Protein | Mass: 20896.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04228 |
#4: Protein | Mass: 24781.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31135 |
-Sugars / Non-polymers , 2 types, 20 molecules
#5: Sugar | ChemComp-NAG / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.95 Å3/Da / Density % sol: 75.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 12% PEG 20000, 100mM bicine pH9.0, 20% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 32259 / % possible obs: 99.7 % / Redundancy: 6.3 % / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 3.1→3.3 Å |
-Processing
Software |
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Refinement | Resolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.841 / SU B: 21.205 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R: 0.713 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.541 Å2
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Refinement step | Cycle: 1 / Resolution: 3.1→50.01 Å
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Refine LS restraints |
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