+Open data
-Basic information
Entry | Database: PDB / ID: 5fdw | ||||||
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Title | Structure of HLA-A2:01 with peptide Y10L | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / Peptide complex | ||||||
Function / homology | Function and homology information T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / positive regulation of type II interferon production / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / endoplasmic reticulum membrane / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / Golgi apparatus / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 5fdw.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fdw.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fdw_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 5fdw_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | 5fdw_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5fdw_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fdw ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fdw | HTTPS FTP |
-Related structure data
Related structure data | 5enwC 5eotC 5f7dC 5f9jC 5fa3C 5fa4C 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 gel filtration |
-Components
#1: Protein | Mass: 31725.088 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1073.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote) |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.64 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 30% PEG 4000, 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: ALS / Beamline: 12.3.1 / Wavelength: 0.73, 2.5 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2015 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. all: 32562 / Num. obs: 11732 / % possible obs: 93.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.89 | |||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MRE Resolution: 2.7→48.18 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.828 / SU B: 14.102 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / 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: 19.796 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→48.18 Å
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