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- PDB-3h9h: Human Class I MHC HLA-A2(A150P) in complex with the Tel1p peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h9h | ||||||
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Title | Human Class I MHC HLA-A2(A150P) in complex with the Tel1p peptide | ||||||
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![]() | IMMUNE SYSTEM / Tel1p peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted | ||||||
Function / homology | ![]() DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Pexophagy / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / phosphatidylinositol-4-phosphate binding / 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 ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Pexophagy / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / phosphatidylinositol-4-phosphate binding / 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 / telomeric DNA binding / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / signal transduction in response to DNA damage / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / negative regulation of TORC1 signaling / telomere maintenance / 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 / negative regulation of receptor binding / DAP12 interactions / DNA damage checkpoint signaling / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 type II interferon production / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / double-strand break repair / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / chromatin organization / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / chromosome, telomeric region / learning or memory / non-specific serine/threonine protein kinase / protein kinase activity / defense response to Gram-positive bacterium / immune response Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Borbulevych, O.Y. / Baker, B.M. | ||||||
![]() | ![]() Title: T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility. Authors: Borbulevych, O.Y. / Piepenbrink, K.H. / Gloor, B.E. / Scott, D.R. / Sommese, R.F. / Cole, D.K. / Sewell, A.K. / Baker, B.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 | ![]() | 183.3 KB | Display | ![]() |
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PDB format | ![]() | 145.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3h7bC ![]() 3h9sC ![]() 3ixaC ![]() 1tvbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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Components
#1: Protein | Mass: 31880.238 Da / Num. of mol.: 2 / Mutation: A150P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1172.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P38110*PLUS #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG3350 24%, MES 0.025M, NaF 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 19, 2008 |
Radiation | Monochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 57629 / Num. obs: 56073 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.069 / Χ2: 0.717 / Net I/σ(I): 16.54 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.52 / Num. unique all: 4973 / Χ2: 0.602 / % possible all: 86.3 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TVB Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.172 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.856 / SU B: 8.006 / SU ML: 0.116 / SU R Cruickshank DPI: 0.197 / SU Rfree: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.185 / ESU R Free: 0.169 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.18 Å2 / Biso mean: 36.521 Å2 / Biso min: 22.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.055 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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