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Yorodumi- PDB-1a1o: MHC CLASS I MOLECULE B*5301 COMPLEXED WITH PEPTIDE LS6 (KPIVQYDNF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a1o | ||||||
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Title | MHC CLASS I MOLECULE B*5301 COMPLEXED WITH PEPTIDE LS6 (KPIVQYDNF) FROM THE MALARIA PARASITE P. FALCIPARUM | ||||||
Components |
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Keywords | COMPLEX (ANTIGEN/PEPTIDE) / MAJOR HISTOCOMPATIBILITY ANTIGEN / MHC / HLA / HLA-B53 / MALARIA / COMPLEX (ANTIGEN-PEPTIDE) / COMPLEX (ANTIGEN-PEPTIDE) complex | ||||||
Function / homology | Function and homology information regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / defense response / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / 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 / 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 / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Smith, K.J. / Reid, S.W. / Harlos, K. / Mcmichael, A.J. / Stuart, D.I. / Bell, J.I. / Jones, E.Y. | ||||||
Citation | Journal: Immunity / Year: 1996 Title: Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53. Authors: Smith, K.J. / Reid, S.W. / Harlos, K. / McMichael, A.J. / Stuart, D.I. / Bell, J.I. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a1o.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a1o.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a1o ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a1o | HTTPS FTP |
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-Related structure data
Related structure data | 1a1mC 1hsaS 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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-Components
#1: Protein | Mass: 32006.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: T7 / Plasmid: BL21 / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P30491, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: T7 / Plasmid: BL21 / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1124.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LS6 FROM THE NEF PROTEIN (75-82) OF HIV-1 / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 18% PEG8000 0.1M SODIUM CACODYLATE PH6.5 0.2M CALCIUM ACETATE | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.97 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 9, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 27424 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 |
Reflection | *PLUS Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HSA Resolution: 2.3→15 Å
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Displacement parameters | Biso mean: 29.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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