+Open data
-Basic information
Entry | Database: PDB / ID: 7jwi | ||||||
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Title | Crystal structure of B17.R2 TCR in complex with H2D-b-NP366 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / TCR / MHC | ||||||
Function / homology | Function and homology information helical viral capsid / 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 ...helical viral capsid / 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 / 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 / viral penetration into host nucleus / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / host cell / 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 / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / ribonucleoprotein complex / symbiont entry into host cell / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / 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 / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å | ||||||
Authors | Farenc, C. / Rossjohn, J. | ||||||
Citation | Journal: Science / Year: 2021 Title: Canonical T cell receptor docking on peptide-MHC is essential for T cell signaling. Authors: Zareie, P. / Szeto, C. / Farenc, C. / Gunasinghe, S.D. / Kolawole, E.M. / Nguyen, A. / Blyth, C. / Sng, X.Y.X. / Li, J. / Jones, C.M. / Fulcher, A.J. / Jacobs, J.R. / Wei, Q. / Wojciech, L. ...Authors: Zareie, P. / Szeto, C. / Farenc, C. / Gunasinghe, S.D. / Kolawole, E.M. / Nguyen, A. / Blyth, C. / Sng, X.Y.X. / Li, J. / Jones, C.M. / Fulcher, A.J. / Jacobs, J.R. / Wei, Q. / Wojciech, L. / Petersen, J. / Gascoigne, N.R.J. / Evavold, B.D. / Gaus, K. / Gras, S. / Rossjohn, J. / La Gruta, N.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jwi.cif.gz | 184.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jwi.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 7jwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jwi_validation.pdf.gz | 475.3 KB | Display | wwPDB validaton report |
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Full document | 7jwi_full_validation.pdf.gz | 480.5 KB | Display | |
Data in XML | 7jwi_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 7jwi_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/7jwi ftp://data.pdbj.org/pub/pdb/validation_reports/jw/7jwi | HTTPS FTP |
-Related structure data
Related structure data | 7jwjC 5swzS 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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1 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABDE
#1: Protein | Mass: 40885.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 |
#4: Protein | Mass: 23117.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) |
#5: Protein | Mass: 27868.260 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) |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1026.099 Da / Num. of mol.: 1 / Fragment: NP-366 epitope (UNP residues 366-374) / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q9Q0U8 |
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-Non-polymers , 2 types, 91 molecules
#6: Chemical | ChemComp-EDO / |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 3.36 Å3/Da / Density % sol: 63.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG3350, 0.2 M potassium/sodium tartrate, 0.1 M Bis-tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→44.27 Å / Num. obs: 28123 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.99 / Net I/σ(I): 11.53 |
Reflection shell | Resolution: 3.02→3.13 Å / Mean I/σ(I) obs: 1.82 / Num. unique obs: 2781 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5SWZ Resolution: 3.02→44.27 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 63.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.49 Å | ||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.02→44.27 Å
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LS refinement shell | Resolution: 3.02→3.04 Å / Rfactor Rfree error: 0
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