+Open data
-Basic information
Entry | Database: PDB / ID: 1sys | ||||||
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Title | Crystal structure of HLA, B*4403, and peptide EEPTVIKKY | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / MHC / Class I / B44 | ||||||
Function / homology | Function and homology information retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retrograde transport, endosome to Golgi / regulation of T cell anergy ...retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retrograde transport, endosome to Golgi / regulation of T cell anergy / regulation of interleukin-6 production / phagocytic cup / Golgi Associated Vesicle Biogenesis / dynactin binding / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / TAP binding / protection from natural killer cell mediated cytotoxicity / ruffle / 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 / phosphatidylinositol binding / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / intracellular protein transport / 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 / defense response / 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 / cytoplasmic side of plasma membrane / 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 / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / 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 / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / endosome / immune response / cadherin binding / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Zernich, D. / Purcell, A.W. / Macdonald, W.A. / Kjer-Nielsen, L. / Ely, L.K. / Laham, N. / Crockford, T. / Mifsud, N.A. / Tait, B.D. / Holdsworth, R. ...Zernich, D. / Purcell, A.W. / Macdonald, W.A. / Kjer-Nielsen, L. / Ely, L.K. / Laham, N. / Crockford, T. / Mifsud, N.A. / Tait, B.D. / Holdsworth, R. / Brooks, A.G. / Bottomley, S.P. / Beddoe, T. / Peh, C.A. / Rossjohn, J. / McCluskey, J. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2004 Title: Natural HLA class I polymorphism controls the pathway of antigen presentation and susceptibility to viral evasion Authors: Zernich, D. / Purcell, A.W. / Macdonald, W.A. / Kjer-Nielsen, L. / Ely, L.K. / Laham, N. / Crockford, T. / Mifsud, N.A. / Bharadwaj, M. / Chang, L. / Tait, B.D. / Holdsworth, R. / Brooks, A. ...Authors: Zernich, D. / Purcell, A.W. / Macdonald, W.A. / Kjer-Nielsen, L. / Ely, L.K. / Laham, N. / Crockford, T. / Mifsud, N.A. / Bharadwaj, M. / Chang, L. / Tait, B.D. / Holdsworth, R. / Brooks, A.G. / Bottomley, S.P. / Beddoe, T. / Peh, C.A. / Rossjohn, J. / McCluskey, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sys.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sys.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/1sys ftp://data.pdbj.org/pub/pdb/validation_reports/sy/1sys | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31978.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30481, UniProt: P01889*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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1108.283 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: Q9Y5X3 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 4000, 0.2M Ammonium Acetate, 0.2M Sodium Citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45 Å / Num. obs: 18236 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45 Å /
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Refinement step | Cycle: LAST / Resolution: 2.4→45 Å
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