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- PDB-7wj2: Crystal structure of HLA-C*1402 complexed with 8-mer HIV gag peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wj2 | |||||||||||||||
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Title | Crystal structure of HLA-C*1402 complexed with 8-mer HIV gag peptide | |||||||||||||||
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Function / homology | ![]() positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Kuroha, J. / Morita, D. / Asa, M. / Sugita, M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding. Authors: Asa, M. / Morita, D. / Kuroha, J. / Mizutani, T. / Mori, N. / 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 | ![]() | 205.5 KB | Display | ![]() |
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PDB format | ![]() | 154.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7wj3C ![]() 7wt3C ![]() 7wt4C ![]() 7wt5C ![]() 5w6aS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32012.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11819.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 894.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 343 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-ACT / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 100 mM sodium acetate, 20 % PEG Smear Low |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.28→50 Å / Num. obs: 96254 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 13.59 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.28→1.3 Å / Rmerge(I) obs: 0.384 / Num. unique obs: 4687 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5W6A Resolution: 1.28→38.44 Å / SU ML: 0.1254 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.8176 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→38.44 Å
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Refine LS restraints |
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LS refinement shell |
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