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Yorodumi- PDB-1eey: Crystal Structure Determination Of HLA A2 Complexed to Peptide GP... -
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-Basic information
Entry | Database: PDB / ID: 1eey | ||||||
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Title | Crystal Structure Determination Of HLA A2 Complexed to Peptide GP2 with the substitution (I2L/V5L/L9V) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / major histicompatibility complex / peptide binding | ||||||
Function / homology | Function and homology information : / : / retina homeostasis / regulation of membrane depolarization / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna ...: / : / retina homeostasis / regulation of membrane depolarization / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / T cell receptor binding / 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 / negative regulation of forebrain neuron differentiation / 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / 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 / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Sharma, A.K. / Kuhns, J.J. / Collins, E.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Class I major histocompatibility complex anchor substitutions alter the conformation of T cell receptor contacts. Authors: Sharma, A.K. / Kuhns, J.J. / Yan, S. / Friedline, R.H. / Long, B. / Tisch, R. / Collins, E.J. #1: Journal: J.Biol.Chem. / Year: 1999 Title: Poor Binding of HER-2/neu Epitope (GP2) to HLA-A2.1 is Due to a Lack of Interactions with the Center of the Peptide Authors: Kuhns, J.J. / Batalia, M.A. / Yan, S. / 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 | 1eey.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eey.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 1eey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1eey ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1eey | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | HLA A2 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy chain is made of three subunits alpha1, alpha 2 and alpha 3. Peptide binds to the groove formed by the alpha1 and alpha2 domains. |
-Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-275 OF EXTRACELLULAR PORTION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid details: PLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid details: PLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01884, UniProt: P61769*PLUS #3: Protein/peptide | Mass: 884.115 Da / Num. of mol.: 2 / Mutation: I2L,V5L,L9V / Source method: obtained synthetically Details: The peptide was synthesized at the peptide synthesis facility of University of North Carolina at Chapel Hill. #4: Water | ChemComp-HOH / | Compound details | HLA A2 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy ...HLA A2 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy chain is made of three subunits alpha1, alpha 2 and alpha 3. Peptide binds to the groove formed by the alpha1 and alpha2 domains. | |
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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: 2.49 Å3/Da / Density % sol: 50.61 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14% PEG 8000, 25 mM MES, pH6.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
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: May 3, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 86999 / Num. obs: 38096 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.07 |
Reflection shell | Resolution: 2.25→2.39 Å / Redundancy: 2 % / Rmerge(I) obs: 0.18 / Num. unique all: 5027 / % possible all: 77.8 |
Reflection | *PLUS Num. measured all: 214687 |
Reflection shell | *PLUS % possible obs: 72 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.7 |
-Processing
Software |
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Refinement | Resolution: 2.25→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1060563.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood function
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.69 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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