[English] 日本語
Yorodumi- PDB-3rwc: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rwc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / antigenic peptides / T lymphocytes / immune response | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide antigen via MHC class I / 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 / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane ...antigen processing and presentation of peptide antigen via MHC class I / 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 / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / 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 / early endosome membrane / late endosome membrane / receptor-mediated endocytosis of virus by host cell / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / virus-mediated perturbation of host defense response / GTP binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Macaca mulatta (Rhesus monkey) Simian immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.502 Å | ||||||
Authors | Wu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Price, D.A. / Gao, G.F. | ||||||
Citation | Journal: J.Immunol. / Year: 2011 Title: Structural basis of diverse peptide accommodation by the rhesus macaque MHC class I molecule Mamu-B*17: insights into immune protection from simian immunodeficiency virus Authors: Wu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Gostick, E. / Price, D.A. / Gao, G.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3rwc.cif.gz | 334.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3rwc.ent.gz | 271.6 KB | Display | PDB format |
PDBx/mmJSON format | 3rwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rwc_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3rwc_full_validation.pdf.gz | 457.4 KB | Display | |
Data in XML | 3rwc_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 3rwc_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/3rwc ftp://data.pdbj.org/pub/pdb/validation_reports/rw/3rwc | HTTPS FTP |
-Related structure data
Related structure data | 3rwdC 3rweC 3rwfC 3rwgC 3rwhC 3rwiC 3rwjC 2bvoS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32025.082 Da / Num. of mol.: 2 / Fragment: residues 24-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: MHCI-B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GJ77 #2: Protein | Mass: 11660.079 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V7J5 #3: Protein/peptide | Mass: 1169.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthtic peptide / Source: (synth.) Simian immunodeficiency virus / References: UniProt: Q5QGG3 #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.21 % |
---|
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
---|---|
Detector | Detector: IMAGE PLATE / Date: Jun 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 32603 / Biso Wilson estimate: 28.72 Å2 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6.2_432) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BVO Resolution: 2.502→27.012 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.809 / SU ML: 0.41 / σ(F): 1.97 / Phase error: 26.41 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.044 Å2 / ksol: 0.332 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.51 Å2 / Biso mean: 30.8969 Å2 / Biso min: 3.47 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.502→27.012 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -0.9029 Å / Origin y: -8.7053 Å / Origin z: -19.3753 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|