+Open data
-Basic information
Entry | Database: PDB / ID: 7t2b | ||||||
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Title | Crystal structure of the 5F TCR in complex with HLA-DP4-Ply | ||||||
Components |
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Keywords | IMMUNE SYSTEM / TCR-pHLA complex | ||||||
Function / homology | Function and homology information MHC class II receptor activity / alpha-beta T cell receptor complex / transport vesicle membrane / cholesterol binding / 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 proliferation ...MHC class II receptor activity / alpha-beta T cell receptor complex / transport vesicle membrane / cholesterol binding / 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 proliferation / immunoglobulin complex, circulating / immunoglobulin receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / complement activation, classical pathway / lumenal side of endoplasmic reticulum membrane / antigen binding / response to bacterium / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cellular response to type II interferon / 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 / endocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of type II interferon production / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / antibacterial humoral response / adaptive immune response / killing of cells of another organism / blood microparticle / immune response / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / host cell plasma membrane / cell surface / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ciacchi, L. / Farenc, C. / Petersen, J. / Reid, H.H. / Rossjohn, J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Immunity / Year: 2023 Title: CD4 + T cell-mediated recognition of a conserved cholesterol-dependent cytolysin epitope generates broad antibacterial immunity. Authors: Ciacchi, L. / van de Garde, M.D.B. / Ladell, K. / Farenc, C. / Poelen, M.C.M. / Miners, K.L. / Llerena, C. / Reid, H.H. / Petersen, J. / Price, D.A. / Rossjohn, J. / van Els, C.A.C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t2b.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7t2b.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7t2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t2b_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7t2b_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7t2b_validation.xml.gz | 104.8 KB | Display | |
Data in CIF | 7t2b_validation.cif.gz | 141.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/7t2b ftp://data.pdbj.org/pub/pdb/validation_reports/t2/7t2b | HTTPS FTP |
-Related structure data
Related structure data | 7t2aC 7t2cC 7t2dC 4p5kS 6cuhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-HLA class II histocompatibility antigen, DP ... , 2 types, 8 molecules AFKPBGLQ
#1: Protein | Mass: 20943.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPA1, HLA-DP1A, HLASB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P20036 #2: Protein | Mass: 22074.725 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPB1, HLA-DP1B / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04440 |
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-Protein/peptide , 1 types, 4 molecules CHMR
#3: Protein/peptide | Mass: 1825.995 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ply, SPD_1726 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q04IN8 |
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-T cell receptor, 5F, ... , 2 types, 8 molecules DINSEJOT
#4: Protein | Mass: 22814.195 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRAC, TCRA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01848 #5: Protein | Mass: 27021.178 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRBC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01850 |
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-Sugars , 2 types, 11 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 19 molecules
#8: Chemical | ChemComp-EDO / #9: Water | ChemComp-HOH / | |
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-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: 2.99 Å3/Da / Density % sol: 58.87 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Tacsimate pH 8, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95365 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.83 Å / Num. obs: 118241 / % possible obs: 99.6 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 11691 / CC1/2: 0.776 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P5K, 6CUH Resolution: 2.8→48.83 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 235.49 Å2 / Biso mean: 72.8446 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→48.83 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -1.095 Å / Origin y: -27.7449 Å / Origin z: 50.2536 Å
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Refinement TLS group |
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