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Yorodumi- PDB-3bgm: Crystal Structure of PKD2 Phosphopeptide Bound to Human Class I M... -
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-Basic information
Entry | Database: PDB / ID: 3bgm | ||||||
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Title | Crystal Structure of PKD2 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 / KINASE / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE | ||||||
Function / homology | Function and homology information protein kinase C / positive regulation of fibroblast growth factor receptor signaling pathway / diacylglycerol-dependent serine/threonine kinase activity / endothelial tube morphogenesis / sphingolipid biosynthetic process / regulation of T cell apoptotic process / Sphingolipid de novo biosynthesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell chemotaxis / T cell mediated cytotoxicity directed against tumor cell target ...protein kinase C / positive regulation of fibroblast growth factor receptor signaling pathway / diacylglycerol-dependent serine/threonine kinase activity / endothelial tube morphogenesis / sphingolipid biosynthetic process / regulation of T cell apoptotic process / Sphingolipid de novo biosynthesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell chemotaxis / 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 / positive regulation of DNA biosynthetic process / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / positive regulation of T cell receptor signaling pathway / 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 / positive regulation of cell adhesion / protection from natural killer cell mediated cytotoxicity / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / beta-2-microglobulin binding / vascular endothelial growth factor receptor signaling pathway / T cell receptor binding / detection of bacterium / positive regulation of endothelial cell proliferation / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / 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 / positive regulation of interleukin-8 production / 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 / protein kinase C binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptidyl-threonine phosphorylation / 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 / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 angiogenesis / 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 / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 3bgm.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bgm.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bgm_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 3bgm_full_validation.pdf.gz | 452.4 KB | Display | |
Data in XML | 3bgm_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 3bgm_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/3bgm ftp://data.pdbj.org/pub/pdb/validation_reports/bg/3bgm | HTTPS FTP |
-Related structure data
Related structure data | 3bh8C 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: 1041.074 Da / Num. of mol.: 1 / Fragment: UNP residues 526-534 / Source method: obtained synthetically / Details: Commercial Synthesis / References: UniProt: Q9BZL6 | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.53 % |
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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 2, 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: 59358 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 26.066 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.95 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.63 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.745 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / 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: 19.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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