+Open data
-Basic information
Entry | Database: PDB / ID: 5eot | ||||||
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Title | Structure of HLA-A2:01 with peptide G13E | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Peptide complex / MHC | ||||||
Function / homology | Function and homology information T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor 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 / lumenal side of endoplasmic reticulum membrane / 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 / positive regulation of immune response / Interferon gamma signaling / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / 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 / cell surface / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zajonc, D.M. / Remesh, S.G. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT. Authors: Remesh, S.G. / Andreatta, M. / Ying, G. / Kaever, T. / Nielsen, M. / McMurtrey, C. / Hildebrand, W. / Peters, B. / Zajonc, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eot.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eot.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 5eot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/5eot ftp://data.pdbj.org/pub/pdb/validation_reports/eo/5eot | HTTPS FTP |
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-Related structure data
Related structure data | 5enwC 5f7dC 5f9jC 5fa3C 5fa4C 5fdwC 3mreS 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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Details | Trimer according to gel filtration |
-Components
#1: Protein | Mass: 31668.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS |
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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 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1022.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 30% PEG 5000 MME, 0.1M Tris-HCl pH 8.0, 0.2M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 26570 / % possible obs: 99.6 % / Redundancy: 3.6 % / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MRE Resolution: 2.1→39.68 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.998 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.283 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→39.68 Å
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