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Yorodumi- PDB-3bh8: Crystal Structure of RQA_M Phosphopeptide Bound to HUMAN Class I ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bh8 | ||||||
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Title | Crystal Structure of RQA_M Phosphopeptide Bound to HUMAN Class I MHC HLA-A2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / PHOSPHOSERINE / PHOSPHOPEPTIDE / MHC / HLA-A2 / ANCHOR RESIDUE / TUMOR ANTIGEN / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE / MHC I / POLYMORPHISM / TRANSMEMBRANE / UBL CONJUGATION / IMMUNOGLOBULIN DOMAIN / PHOSPHOPROTEIN | ||||||
Function / homology | Function and homology information cellular response to interleukin-7 / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I ...cellular response to interleukin-7 / 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 / 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 / beta-2-microglobulin binding / cellular defense response / 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 / 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 / chemotaxis / 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 / actin cytoskeleton / 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 / actin binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / 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 / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Mohammed, F. / Cobbold, M. / Zarling, A.L. / Salim, M. / Barrett-Wilt, G.A. / Shabanowitz, J. / Hunt, D.F. / Engelhard, V.H. / Willcox, B.E. | ||||||
Citation | Journal: Nat.Immunol. / Year: 2008 Title: Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self Authors: Mohammed, F. / Cobbold, M. / Zarling, A.L. / Salim, M. / Barrett-Wilt, G.A. / Shabanowitz, J. / Hunt, D.F. / Engelhard, V.H. / Willcox, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bh8.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bh8.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bh8_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 3bh8_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 3bh8_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 3bh8_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/3bh8 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/3bh8 | HTTPS FTP |
-Related structure data
Related structure data | 3bgmC 3bh9C 3bhbC 3bha C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31725.088 Da / Num. of mol.: 1 / Fragment: Alpha-1, Alpha-2, Alpha-3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01892, UniProt: P04439*PLUS | ||||
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769 | ||||
#3: Protein/peptide | Mass: 1212.290 Da / Num. of mol.: 1 / Fragment: UNP residues 249-258 / Source method: obtained synthetically / Details: COMMERCIAL SYNTHESIS / References: UniProt: P33241 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 17% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: SATURN / Detector: CCD / Date: Apr 3, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→20 Å / Num. obs: 53891 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 25.593 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 26.79 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.006 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.944 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→19.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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