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Open data
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Basic information
Entry | Database: PDB / ID: 8sbl | |||||||||
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Title | Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI | |||||||||
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![]() | IMMUNE SYSTEM / Major Histocompatibility Complex (MHC) | |||||||||
Function / homology | ![]() 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 / Endosomal/Vacuolar pathway ...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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / 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 / 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 / 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 / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mallik, L. / Young, M.C. / Sgourakis, N.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Authors: Sun, Y. / Florio, T.J. / Gupta, S. / Young, M.C. / Marshall, Q.F. / Garfinkle, S.E. / Papadaki, G.F. / Truong, H.V. / Mycek, E. / Li, P. / Farrel, A. / Church, N.L. / Jabar, S. / Beasley, M. ...Authors: Sun, Y. / Florio, T.J. / Gupta, S. / Young, M.C. / Marshall, Q.F. / Garfinkle, S.E. / Papadaki, G.F. / Truong, H.V. / Mycek, E. / Li, P. / Farrel, A. / Church, N.L. / Jabar, S. / Beasley, M.D. / Kiefel, B.R. / Yarmarkovich, M. / Mallik, L. / Maris, J.M. / Sgourakis, N.G. #1: Journal: Sci Immunol / Year: 2023 Title: The chilling origin of germinal centers. Authors: Boehm, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.2 KB | Display | ![]() |
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PDB format | ![]() | 253.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.8 KB | Display | ![]() |
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Full document | ![]() | 519.7 KB | Display | |
Data in XML | ![]() | 52.2 KB | Display | |
Data in CIF | ![]() | 71.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ek5C ![]() 8sbkC 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
#1: Protein | Mass: 32466.869 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1086.390 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3→105.19 Å / Num. obs: 34967 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.83 Å2 / CC1/2: 0.877 / R split: 0.341 / Rmerge(I) obs: 0.388 / Rpim(I) all: 0.244 / Rrim(I) all: 0.459 / Χ2: 0.46 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 3.05→3.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.203 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4832 / CC1/2: 0.419 / Rpim(I) all: 0.746 / Rrim(I) all: 1.418 / Χ2: 0.47 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→105.19 Å
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Refine LS restraints |
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LS refinement shell |
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