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- PDB-5iro: Crystal structure of a complex between the Human adenovirus type ... -
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Basic information
Entry | Database: PDB / ID: 5iro | ||||||
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Title | Crystal structure of a complex between the Human adenovirus type 4 E3-19K protein and MHC class molecule HLA-A2/TAX | ||||||
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![]() | Immune system/transcription / Ad4 E3-19K-HLA-A2 COMPLEX / IMMUNE EVASION FUNCTION / MHC CLASS I MOLECULE / Immune system-transcription complex | ||||||
Function / homology | ![]() symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I => GO:0046776 / symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated suppression of host adaptive immune response / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / 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 ...symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I => GO:0046776 / symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated suppression of host adaptive immune response / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / D-mannose binding / 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 / regulation of mRNA stability / 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 / SH3 domain binding / 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 / 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 receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / membrane => GO:0016020 / learning or memory / host cell endoplasmic reticulum membrane / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, L. / Bouvier, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the Adenovirus Type 4 (Species E) E3-19K/HLA-A2 Complex Reveals Species-Specific Features in MHC Class I Recognition. Authors: Li, L. / Santarsiero, B.D. / Bouvier, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 565.9 KB | Display | ![]() |
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PDB format | ![]() | 468.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 550 KB | Display | ![]() |
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Full document | ![]() | 756.9 KB | Display | |
Data in XML | ![]() | 115 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Details | Tetramer confirmed by FPLC gel filtration |
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Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1070.280 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Human T-cell lymphotropic virus type 1, HTLV-1 TAX / Source: (synth.) ![]() #3: Protein | Mass: 11879.356 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 12394.115 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % / Description: Tween crystal Size 0.15X0.07X0.05mm |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6.5 / Details: 1.5M (NH4)2SO4,0.1M Bis-Tris pH6.5, 0.1MNaCI / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.47 |
Reflection | Resolution: 2.64→100 Å / Num. obs: 110878 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.64→2.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HLA-A2 Resolution: 2.64→49.625 Å / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 29.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→49.625 Å
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Refine LS restraints |
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LS refinement shell |
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