+Open data
-Basic information
Entry | Database: PDB / ID: 4l4t | ||||||
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Title | Structure of human MAIT TCR in complex with human MR1-6-FP | ||||||
Components |
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Keywords | Membrane Protein/Immune System / MHC Class I-related protein / MAIT TCR / Immune System / Vitamin B metabolites / Membrane Protein-Immune System complex | ||||||
Function / homology | Function and homology information positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / alpha-beta T cell receptor complex / antigen processing and presentation of peptide antigen via MHC class I / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / alpha-beta T cell receptor complex / antigen processing and presentation of peptide antigen via MHC class I / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Patel, O. / Kjer-Nielsen, L. / Le Nours, J. / Eckle, S.B.G. / Birkinshaw, R.W. / Beddoe, T. / Corbett, A.J. / Liu, L. / Miles, J.J. / Meehan, B. ...Patel, O. / Kjer-Nielsen, L. / Le Nours, J. / Eckle, S.B.G. / Birkinshaw, R.W. / Beddoe, T. / Corbett, A.J. / Liu, L. / Miles, J.J. / Meehan, B. / Reantragoon, R. / Sandoval-Romero, M.L. / Sullivan, L.C. / Brooks, A.G. / Chen, Z. / Fairlie, D.P. / McCluskey, J. / Rossjohn, J. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Recognition of vitamin B metabolites by mucosal-associated invariant T cells. Authors: Patel, O. / Kjer-Nielsen, L. / Le Nours, J. / Eckle, S.B. / Birkinshaw, R. / Beddoe, T. / Corbett, A.J. / Liu, L. / Miles, J.J. / Meehan, B. / Reantragoon, R. / Sandoval-Romero, M.L. / ...Authors: Patel, O. / Kjer-Nielsen, L. / Le Nours, J. / Eckle, S.B. / Birkinshaw, R. / Beddoe, T. / Corbett, A.J. / Liu, L. / Miles, J.J. / Meehan, B. / Reantragoon, R. / Sandoval-Romero, M.L. / Sullivan, L.C. / Brooks, A.G. / Chen, Z. / Fairlie, D.P. / McCluskey, J. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l4t.cif.gz | 355 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l4t.ent.gz | 284.9 KB | Display | PDB format |
PDBx/mmJSON format | 4l4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/4l4t ftp://data.pdbj.org/pub/pdb/validation_reports/l4/4l4t | HTTPS FTP |
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-Related structure data
Related structure data | 4l4vC 4gupS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBF
#1: Protein | Mass: 31711.670 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 23-292 / Mutation: C261S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q95460 #2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 |
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-MAIT T-cell receptor ... , 2 types, 4 molecules DGEH
#3: Protein | Mass: 22650.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TCR alpha / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 #4: Protein | Mass: 27546.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TCR beta / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01850*PLUS |
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-Non-polymers , 2 types, 1295 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: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 139624 / Num. obs: 139624 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 27.16 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.1 / Num. unique all: 20300 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4GUP Resolution: 2→49.38 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.9113 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.72 Å2
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Refine analyze | Luzzati coordinate error obs: 0.225 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→49.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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