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Yorodumi- PDB-1i1f: Crystal structure of human class i mhc (hla-a2.1) complexed with ... -
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-Basic information
Entry | Database: PDB / ID: 1i1f | ||||||
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Title | Crystal structure of human class i mhc (hla-a2.1) complexed with beta 2-microglobulin and hiv-rt variant peptide i1y | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HUMAN CLASS I MHC / HIV | ||||||
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 / 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 / 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 / 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 / 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 / detection of bacterium / T cell 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 / 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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / 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 / recycling endosome membrane / specific granule lumen / 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 / positive regulation of type II interferon production / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / 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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kirksey, T.J. / Pogue-Caley, R.R. / Frelinger, J.A. / Collins, E.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The structural basis for the increased immunogenicity of two HIV-reverse transcriptase peptide variant/class I major histocompatibility complexes. Authors: Kirksey, T.J. / Pogue-Caley, R.R. / Frelinger, J.A. / Collins, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i1f.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i1f.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 1i1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1f ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1f | HTTPS FTP |
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-Related structure data
Related structure data | 1i1yC 1hhhS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.91, 0.4146, 0.0008), Vector: |
-Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: PEPTIDE-BINDING DOMAIN + ALPHA3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: BETA 2-MICROGLOBULIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P61769 #3: Protein/peptide | Mass: 1027.215 Da / Num. of mol.: 2 / Fragment: RESIDUES 309-317 / Mutation: I1F / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 46 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 16% PEG8000 IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE OF THE ...Details: PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 16% PEG8000 IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE OF THE RESERVOIR SOLUTION AND THE PROTEIN SOLUTION WHICH CONTAINED 10MG/ML PROTEIN IN 25MM MES BUFFER, PH6.5. | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of 1:1 mixture of well and protein solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 21030 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.2 / % possible all: 98.6 |
Reflection | *PLUS Num. measured all: 148065 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHH Resolution: 2.8→15 Å / SU B: 0.2 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.53
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Displacement parameters | Biso mean: 43.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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