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Yorodumi- PDB-1im3: Crystal Structure of the human cytomegalovirus protein US2 bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1im3 | ||||||
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Title | Crystal Structure of the human cytomegalovirus protein US2 bound to the MHC class I molecule HLA-A2/tax | ||||||
Components |
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Keywords | Viral protein/Immune system / Beta sheet / Beta sandwhich / Immunoglobulin (Ig) fold / immunoglobulin (IG)-like domain / protein complex / alpha helix / Viral protein-Immune system COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / virus-mediated perturbation of host defense response => GO:0019049 / 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 ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / virus-mediated perturbation of host defense response => GO:0019049 / 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 / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / SH3 domain binding / 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 / 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 / Golgi membrane / lysosomal membrane / external side of plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human herpesvirus 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Gewurz, B.E. / Gaudet, R. / Tortorella, D. / Wang, E.W. / Ploegh, H.L. / Wiley, D.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Antigen presentation subverted: Structure of the human cytomegalovirus protein US2 bound to the class I molecule HLA-A2. Authors: Gewurz, B.E. / Gaudet, R. / Tortorella, D. / Wang, E.W. / Ploegh, H.L. / Wiley, D.C. #1: Journal: J.Virol. / Year: 2001 Title: Human cytomegalovirus US2 endoplasmic reticulum-lumenal domain dictates association with major histocompatibility complex class I in a locus-specific manner Authors: Gewurz, B.E. / Wang, E.W. / Tortorella, D. / Schust, D.S. / Ploegh, H.L. #2: Journal: J.Immunol. / Year: 2000 Title: The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site Authors: Khan, A.R. / Baker, B.M. / Ghosh, B. / E Biddison, W. / Wiley, D.C. #3: Journal: Nature / Year: 1996 Title: Sec61-mediated transfer of a membrane protein from the endoplasmic reticulum to the proteasome for destruction Authors: Wiertz, E.J. / Tortorella, D. / Bogyo, M. / Rapoport, T.A. / Ploegh, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1im3.cif.gz | 424.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1im3.ent.gz | 344.8 KB | Display | PDB format |
PDBx/mmJSON format | 1im3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1im3_validation.pdf.gz | 526 KB | Display | wwPDB validaton report |
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Full document | 1im3_full_validation.pdf.gz | 549.9 KB | Display | |
Data in XML | 1im3_validation.xml.gz | 84 KB | Display | |
Data in CIF | 1im3_validation.cif.gz | 121.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/1im3 ftp://data.pdbj.org/pub/pdb/validation_reports/im/1im3 | HTTPS FTP |
-Related structure data
Related structure data | 1duzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 4 / Fragment: extracellular domain, heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A2 / Plasmid: pET27 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: recombinant residues 1-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Beta 2-microglobulin / Plasmid: Plm-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1070.280 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: HTLV Tax peptide (LLFGYPVYV) was produced by FMOC solid phase peptide synthesis References: GenBank: 699503, UniProt: P14079*PLUS #4: Protein | Mass: 10899.435 Da / Num. of mol.: 4 / Fragment: recombinant ER-lumenal fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Gene: US2 / Plasmid: pET27d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09713 #5: Water | ChemComp-HOH / | |
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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: 3.25 Å3/Da / Density % sol: 62.15 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: PEG 6000, MPD, Tris, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 139486 / Num. obs: 139486 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.3 / Num. unique all: 13849 / % possible all: 97.1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Num. obs: 13849 / Num. measured all: 139486 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 97.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1DUZ Resolution: 2.2→38.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 387634.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.11 Å2 / ksol: 0.32 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→38.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 2 % / Rfactor Rfree: 0.24 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 40.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.348 / % reflection Rfree: 2 % / Rfactor Rwork: 0.3 / Rfactor obs: 0.3 |