[English] 日本語
Yorodumi- PDB-1i1y: CRYSTAL STRUCTURE OF HUMAN CLASS I MHC (HLA-A2.1) COMPLEXED WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i1y | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN CLASS I MHC (HLA-A2.1) COMPLEXED WITH BETA 2-MICROGLOBULIN AND HIV-RT VARIANT PEPTIDE I1Y | ||||||
Components |
| ||||||
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 / 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 / DAP12 interactions / negative regulation of 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / 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 / Interferon alpha/beta signaling / positive regulation of type II interferon production / 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 receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / 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 / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kirksey, T.J. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1i1y.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1i1y.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 1i1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i1y_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1i1y_full_validation.pdf.gz | 485.5 KB | Display | |
Data in XML | 1i1y_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 1i1y_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1y ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1y | HTTPS FTP |
-Related structure data
Related structure data | 1i1fC 1hhhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.915475, 0.402374, -0.000847), 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 / Cellular location (production host): INCLUSION BODIES / 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 / Cellular location (production host): INCLUSION BODY / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P61769 #3: Protein/peptide | Mass: 1043.215 Da / Num. of mol.: 2 / Fragment: RESIDUES 309-317 / Mutation: I1Y / Source method: obtained synthetically #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 18% 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 18% 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., pH 6.50, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of 1:1 mixture of well and protein solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0789 |
Detector | Type: ADSC / Detector: CCD / Date: May 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0789 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 45024 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 23.1 / % possible all: 96.4 |
Reflection | *PLUS % possible obs: 97.9 % / Num. measured all: 222078 |
Reflection shell | *PLUS % possible obs: 96.4 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHH Resolution: 2.2→15 Å / SU B: 7.8 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.26
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|