+Open data
-Basic information
Entry | Database: PDB / ID: 6dfw | ||||||
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Title | TCR 8F10 in complex with IAg7-p8G9E | ||||||
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 / negative regulation of T cell proliferation / antigen processing and presentation / 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 ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / negative regulation of T cell proliferation / antigen processing and presentation / 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 / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 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 | 6dfw.cif.gz | 630.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dfw.ent.gz | 540.6 KB | Display | PDB format |
PDBx/mmJSON format | 6dfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/6dfw ftp://data.pdbj.org/pub/pdb/validation_reports/df/6dfw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 20907.348 Da / Num. of mol.: 2 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 #2: Protein | Mass: 25290.279 Da / Num. of mol.: 2 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 #3: Protein | Mass: 23405.010 Da / Num. of mol.: 2 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 #4: Protein | Mass: 26880.781 Da / Num. of mol.: 2 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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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 3350, 100mM formate pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 38891 / % possible obs: 96.9 % / Redundancy: 3.4 % / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.2→3.5 Å |
-Processing
Software |
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Refinement | Resolution: 3.2→50.01 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.886 / SU B: 97.35 / SU ML: 0.69 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 132.243 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→50.01 Å
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Refine LS restraints |
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