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- PDB-6lt6: 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: 6lt6 | ||||||||||||||||||
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Title | Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with lysophosphatidylcholine | ||||||||||||||||||
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![]() | IMMUNE SYSTEM / MHC class I protein / complex / lysophospholipid | ||||||||||||||||||
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 / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / extracellular space / extracellular region Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Shima, Y. / Morita, D. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of lysophospholipid-bound MHC class I molecules. Authors: Shima, Y. / Morita, D. / 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 | ![]() | 102.5 KB | Display | ![]() |
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PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 603.1 KB | Display | ![]() |
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Full document | ![]() | 606.2 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lahC ![]() 6lamC ![]() 6lb2C ![]() 6iwgS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31905.137 Da / Num. of mol.: 1 / Mutation: R128E, K177E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11731.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 218 molecules ![](data/chem/img/EKG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EKG / ( | ||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.13 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Bis-Tris propane, 0.2M Sodium malonate dibasic monohydrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 25511 / % possible obs: 96 % / Redundancy: 7.7 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 2.15→2.19 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.83 / Num. unique obs: 1228 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6IWG Resolution: 2.15→45.19 Å / SU ML: 0.2932 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.959 / Stereochemistry target values: 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: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→45.19 Å
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Refine LS restraints |
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LS refinement shell |
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