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Open data
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Basic information
Entry | Database: PDB / ID: 4nnx | ||||||
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Title | Crystal structure of PKD2 phosphopeptide bound to HLA-A2 | ||||||
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![]() | IMMUNE SYSTEM/ANTIGEN / phosphoserine / phosphopeptide / MHC / post translational modification / tumor immunology / tumor antigens / neoepitope / IMMUNE SYSTEM-ANTIGEN complex | ||||||
Function / homology | ![]() 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 / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of DNA biosynthetic process / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / positive regulation of interleukin-8 production / 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 / protein kinase C binding / 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 / 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 / positive regulation of DNA-binding transcription factor activity / 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 / positive regulation of angiogenesis / 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 / 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 / positive regulation of NF-kappaB transcription factor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mohammed, F. / Stones, D.H. / Willcox, B.E. | ||||||
![]() | ![]() Title: The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status. Authors: Mohammed, F. / Stones, D.H. / Zarling, A.L. / Willcox, C.R. / Shabanowitz, J. / Cummings, K.L. / Hunt, D.F. / Cobbold, M. / Engelhard, V.H. / Willcox, B.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.2 KB | Display | ![]() |
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PDB format | ![]() | 73.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nnyC ![]() 4no0C ![]() 4no2C ![]() 4no3C ![]() 4no5C ![]() 3bh9S 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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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31725.088 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 25-298) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1041.074 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 526-534) / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 209 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CD / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 11% PEG3350, 0.1 M HEPES, pH 7.5, 0.15 M sodium chloride, 0.003 M magnesium chloride, 0.003 M cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 13, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.104→19.734 Å / Num. obs: 31648 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 24.758 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 15.29 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3BH9 Resolution: 2.104→19.73 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2056 / WRfactor Rwork: 0.1764 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.849 / SU B: 4.164 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1892 / SU Rfree: 0.1686 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.169 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.92 Å2 / Biso mean: 18.6489 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.104→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.104→2.158 Å / Total num. of bins used: 20
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