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- PDB-3pwu: An immmunodominant CTL epitope from rinderpest virus presented by... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pwu | ||||||
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Title | An immmunodominant CTL epitope from rinderpest virus presented by cattle MHC class I molecule N*01801(BoLA-A11) | ||||||
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![]() | IMMUNE SYSTEM / MHC BoLA conformation / immunodominant epitope cattle | ||||||
Function / homology | ![]() antigen processing and presentation of peptide antigen via MHC class I / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell membrane / cellular defense response / Neutrophil degranulation ...antigen processing and presentation of peptide antigen via MHC class I / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell membrane / cellular defense response / Neutrophil degranulation / 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 / 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 / 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 / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / host cell surface receptor binding / symbiont entry into host cell / immune response / lysosomal membrane / external side of plasma membrane / viral envelope / virion attachment to host cell / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Li, X. / Liu, J. / Qi, J. / Gao, F. / Li, Q. / Li, X. / Zhang, N. / Xia, C. / Gao, G.F. | ||||||
![]() | ![]() Title: Two distinct conformations of a rinderpest virus epitope presented by bovine major histocompatibility complex class I N*01801: a host strategy to present featured peptides Authors: Li, X. / Liu, J. / Qi, J. / Gao, F. / Li, Q. / Li, X. / Zhang, N. / Xia, C. / Gao, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 75.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pwvC ![]() 1e27S S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 31797.080 Da / Num. of mol.: 1 / Fragment: residues in UNP 26-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: murine beta2m Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 946.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized artificially / References: UniProt: P41355 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 28, 2010 |
Radiation | Monochromator: Cu Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.899→50 Å / Num. obs: 32536 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 29.174 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3.138 / Num. unique all: 2466 / Rsym value: 0.535 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.121 Å2 / ksol: 0.366 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.899→23.956 Å
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Refine LS restraints |
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LS refinement shell |
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