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- PDB-7n5c: 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n5c | ||||||
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Title | 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond | ||||||
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![]() | IMMUNE SYSTEM / Major Histocompatibility complex / MHC / mouse / Influenza A / polymerase acidic protein / H2Db / T cell receptor / PA224-233 / disulfide bond / Cysteine | ||||||
Function / homology | ![]() cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / endonuclease activity / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / Hydrolases; Acting on ester bonds / learning or memory / cell surface receptor signaling pathway / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / viral RNA genome replication / Golgi membrane / focal adhesion / signaling receptor binding / DNA-templated transcription / host cell nucleus / Neutrophil degranulation / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szeto, C. / Gras, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus. Authors: Szeto, C. / Zareie, P. / Wirasinha, R.C. / Zhang, J.B. / Nguyen, A.T. / Riboldi-Tunnicliffe, A. / La Gruta, N.L. / Gras, S. / Daley, S.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.9 KB | Display | ![]() |
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PDB format | ![]() | 143.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.2 KB | Display | ![]() |
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Full document | ![]() | 473.1 KB | Display | |
Data in XML | ![]() | 31.3 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n4kC ![]() 7n5pC ![]() 7n5qC ![]() 3pqyS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32174.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P01899 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1160.324 Da / Num. of mol.: 1 / Mutation: E4C / Source method: obtained synthetically Details: Polymerase Acidic Protein 224-233 with E227C (E4C) mutation Source: (synth.) ![]() ![]() |
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-Fusion protein of T cell receptor ... , 2 types, 2 molecules DE
#4: Protein | Mass: 22510.906 Da / Num. of mol.: 1 / Mutation: S110C Source method: isolated from a genetically manipulated source Details: 6218 TCR-alpha with S110C mutation Source: (gene. exp.) ![]() ![]() ![]() Gene: Trav21-dv12 Production host: ![]() ![]() References: UniProt: A0A075B6C4, UniProt: K7N5N2 |
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#5: Protein | Mass: 27575.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 6218 TCR beta chain Source: (gene. exp.) ![]() ![]() ![]() Gene: Trbv29, B2M, HDCMA22P Production host: ![]() ![]() References: UniProt: A0A0G2LB96, UniProt: K7N5M4 |
-Non-polymers , 2 types, 262 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-NA / |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 20% PEG3350, 0.2M NaF, 0.05M NaForm, 1% 1,5-Diaminopentane dihydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→47.41 Å / Num. obs: 77867 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 35.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 12.9 / Num. measured all: 546387 / Scaling rejects: 744 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PQY Resolution: 1.87→27.14 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.129
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Displacement parameters | Biso max: 132.21 Å2 / Biso mean: 41.79 Å2 / Biso min: 12.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.87→27.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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