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Yorodumi- PDB-4e5x: Crystal structure of a complex between the human adenovirus type ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e5x | ||||||
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Title | Crystal structure of a complex between the human adenovirus type 2 E3-19K protein and MHC class I molecule HLA-A2/Tax | ||||||
Components |
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Keywords | IMMUNE SYSTEM/TRANSCRIPTION / Ad2 E3-19K-HLA-A2 complex / unique tertiary structure / Adenovirus E3-19K / Immune evasion function / MHC class I molecule / Endoplasmic reticulum / IMMUNE SYSTEM-TRANSCRIPTION complex | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 perturbation of host exit from mitosis / symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / D-mannose binding / 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 / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / sensory perception of smell / MHC class I protein complex / SH3 domain binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / negative regulation of neuron projection development / positive regulation of protein binding / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / antibacterial humoral response / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / host cell endoplasmic reticulum membrane / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human adenovirus 6 Human T-cell lymphotropic virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Li, L. / Bouvier, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Crystal structure of adenovirus E3-19K bound to HLA-A2 reveals mechanism for immunomodulation. Authors: Li, L. / Muzahim, Y. / Bouvier, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e5x.cif.gz | 216.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e5x.ent.gz | 173 KB | Display | PDB format |
PDBx/mmJSON format | 4e5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e5x_validation.pdf.gz | 479.7 KB | Display | wwPDB validaton report |
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Full document | 4e5x_full_validation.pdf.gz | 502.3 KB | Display | |
Data in XML | 4e5x_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 4e5x_validation.cif.gz | 59.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/4e5x ftp://data.pdbj.org/pub/pdb/validation_reports/e5/4e5x | HTTPS FTP |
-Related structure data
Related structure data | 1hhkS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / 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) / Gene: B2M, Beta-2-M, CDABP0092, HDCMA22P / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1070.280 Da / Num. of mol.: 2 / Fragment: Tax peptide / Source method: obtained synthetically / Details: Human T-cell lymphotropic virus type 1 Tax peptide Source: (synth.) Human T-cell lymphotropic virus type 1 (african isolate) References: UniProt: P0C213 #4: Protein | Mass: 11938.821 Da / Num. of mol.: 2 / Fragment: Ad2 e3-19K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus 6 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P68979 #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.48 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 108659 / Num. obs: 108334 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 15.97 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / Num. unique all: 10477 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHK Resolution: 1.95→37.06 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.6 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→37.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.007
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