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Yorodumi- PDB-3pwv: An immmunodominant CTL epitope from rinderpest virus presented by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pwv | ||||||
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Title | An immmunodominant CTL epitope from rinderpest virus presented by cattle MHC class I molecule N*01801 (BoLA-A11) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC BoLA-A11 conformation cattle / immunodominant epitope | ||||||
Function / homology | Function and homology information ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / antigen processing and presentation / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / antigen processing and presentation / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / membrane => GO:0016020 / host cell surface receptor binding / immune response / lysosomal membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Rinderpest virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.696 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pwv.cif.gz | 318 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pwv.ent.gz | 261.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/3pwv ftp://data.pdbj.org/pub/pdb/validation_reports/pw/3pwv | HTTPS FTP |
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-Related structure data
Related structure data | 3pwuC 1e27S S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31797.080 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 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: 11653.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: B2M / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01888 #3: Protein/peptide | Mass: 946.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized artificially / Source: (synth.) Rinderpest virus / References: UniProt: Q9YKD7 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 18, 2010 |
Radiation | Monochromator: Cu Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.696→50 Å / Num. obs: 28833 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 16.186 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 4.302 / Rsym value: 0.548 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+27 / Resolution: 2.696→30.225 Å / SU ML: 0.33 / σ(F): 0.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.776 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.696→30.225 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 11.1723 Å / Origin y: -43.9447 Å / Origin z: -11.2455 Å
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Refinement TLS group | Selection details: all |