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Yorodumi- PDB-1tvh: Crystal structure of Modified Melanoma Antigen gp100(209-T2M) Bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tvh | ||||||
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Title | Crystal structure of Modified Melanoma Antigen gp100(209-T2M) Bound to Human Class I MHC HLA-A2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Melanoma / X-ray / modified gp100 peptide / gp100(209-T2M) peptide / MHC / HLA-A2 | ||||||
Function / homology | Function and homology information positive regulation of melanin biosynthetic process / multivesicular body, internal vesicle / melanin biosynthetic process / melanosome organization / melanosome membrane / multivesicular body membrane / cis-Golgi network membrane / 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 ...positive regulation of melanin biosynthetic process / multivesicular body, internal vesicle / melanin biosynthetic process / melanosome organization / melanosome membrane / multivesicular body membrane / cis-Golgi network membrane / 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 / melanosome / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / 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 / intracellular iron ion homeostasis / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Authors | Borbulevych, O.Y. / Baker, B.M. | ||||||
Citation | Journal: J.Immunol. / Year: 2005 Title: Increased Immunogenicity of an Anchor-Modified Tumor-Associated Antigen Is Due to the Enhanced Stability of the Peptide/MHC Complex: Implications for Vaccine Design Authors: Borbulevych, O.Y. / Baxter, T.K. / Yu, Z. / Restifo, N.P. / Baker, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tvh.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tvh.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 1tvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/1tvh ftp://data.pdbj.org/pub/pdb/validation_reports/tv/1tvh | HTTPS FTP |
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-Related structure data
Related structure data | 1tvbC 1borS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: alpha-chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: beta-chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): pHN1 / References: UniProt: P61769 #3: Protein/peptide | Mass: 1035.213 Da / Num. of mol.: 2 / Fragment: residues 209-217 / Source method: obtained synthetically / Details: a modified sequence occurs naturally in humans / References: UniProt: P40967 #4: Chemical | ChemComp-GOL / #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: 2.3 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98731 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 21, 2004 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98731 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 75145 / Num. obs: 74168 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 17.58 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.72 / Num. unique all: 7284 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1BOR Resolution: 1.802→10 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.5 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.143 / ESU R Free: 0.146 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.467 Å2
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Refinement step | Cycle: LAST / Resolution: 1.802→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.847 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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