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Open data
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Basic information
Entry | Database: PDB / ID: 3rwf | ||||||
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Title | Rhesus macaque MHC class I molecule Mamu-B*17-QW9 | ||||||
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![]() | IMMUNE SYSTEM / antigenic peptides / T lymphocytes / immune response | ||||||
Function / homology | ![]() 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 / late endosome membrane / early endosome membrane / receptor-mediated endocytosis of virus by host cell / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / GTP binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Price, D.A. / Gao, G.F. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.6 KB | Display | ![]() |
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PDB format | ![]() | 138.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.8 KB | Display | ![]() |
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Full document | ![]() | 438 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rwcC ![]() 3rwdC ![]() 3rweC ![]() 3rwgC ![]() 3rwhC ![]() 3rwiC ![]() 3rwjC ![]() 2bvoS 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
#1: Protein | Mass: 32025.082 Da / Num. of mol.: 1 / Fragment: residues 24-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11791.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1162.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthtic peptide / Source: (synth.) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
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-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 13578 / Biso Wilson estimate: 38.78 Å2 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6.2_432) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2BVO Resolution: 2.6→24.639 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.799 / SU ML: 0.42 / σ(F): 1.99 / Phase error: 27.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.132 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.48 Å2 / Biso mean: 43.295 Å2 / Biso min: 6.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→24.639 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: 5 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -26.3939 Å / Origin y: -7.4902 Å / Origin z: -0.1929 Å
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Refinement TLS group |
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