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- PDB-4zfz: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*0... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zfz | ||||||
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Title | Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein | ||||||
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![]() | IMMUNE SYSTEM / MHC / lipopeptide / Antigen presentation / AIDS | ||||||
Function / homology | ![]() virus-mediated perturbation of host defense response => GO:0019049 / antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / : / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response ...virus-mediated perturbation of host defense response => GO:0019049 / antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / : / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / immune response / lysosomal membrane / GTP binding / host cell plasma membrane / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morita, D. / Sugita, M. | ||||||
![]() | ![]() Title: Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex Authors: Morita, D. / Yamamoto, Y. / Mizutani, T. / Ishikawa, T. / Suzuki, J. / Igarashi, T. / Mori, N. / Shiina, T. / Inoko, H. / Fujita, H. / Iwai, K. / Tanaka, Y. / Mikami, B. / Sugita, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354.6 KB | Display | ![]() |
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PDB format | ![]() | 287.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 568.6 KB | Display | ![]() |
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Full document | ![]() | 585.3 KB | Display | |
Data in XML | ![]() | 67.1 KB | Display | |
Data in CIF | ![]() | 93.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rwjS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 8 molecules ADGJBEHK
#1: Protein | Mass: 31687.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11731.157 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 4 molecules CFIL
#3: Protein/peptide | Mass: 403.432 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 6 types, 902 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-MYR / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: Zinc chloride, Tris-HCl, PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 182504 / % possible obs: 96.2 % / Redundancy: 2.61 % / Net I/σ(I): 30.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3RWJ Resolution: 1.763→31.18 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.81 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.763→31.18 Å
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Refine LS restraints |
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LS refinement shell |
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