[English] 日本語
Yorodumi- PDB-3pwu: An immmunodominant CTL epitope from rinderpest virus presented by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pwu | ||||||
---|---|---|---|---|---|---|---|
Title | An immmunodominant CTL epitope from rinderpest virus presented by cattle MHC class I molecule N*01801(BoLA-A11) | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / MHC BoLA conformation / immunodominant epitope cattle | ||||||
Function / homology | Function and homology information 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 / 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 / phagocytic vesicle membrane / 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 / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / 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 / external side of plasma membrane / lysosomal membrane / viral envelope / virion attachment to host cell / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 Å | ||||||
Authors | Li, X. / Liu, J. / Qi, J. / Gao, F. / Li, Q. / Li, X. / Zhang, N. / Xia, C. / Gao, G.F. | ||||||
Citation | Journal: J.Virol. / Year: 2011 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pwu.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pwu.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 3pwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pwu_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3pwu_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 3pwu_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 3pwu_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/3pwu ftp://data.pdbj.org/pub/pdb/validation_reports/pw/3pwu | HTTPS FTP |
-Related structure data
Related structure data | 3pwvC 1e27S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Bos taurus (cattle) / Gene: LA-A11 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95477 |
---|---|
#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: murine beta2m Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887 |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+27 / Resolution: 1.899→23.956 Å / SU ML: 0.25 / σ(F): 0.15 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.899→23.956 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|