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- PDB-6lah: 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: 6lah | ||||||||||||||||||
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Title | Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 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 / external side of plasma membrane / lysosomal membrane / signaling receptor binding / extracellular space / extracellular region / metal ion binding 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 | ![]() | 187.5 KB | Display | ![]() |
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PDB format | ![]() | 143.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6lamC ![]() 6lb2C ![]() 6lt6C ![]() 4zfzS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 31687.727 Da / Num. of mol.: 2 / Mutation: C167S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11731.157 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 451 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EKG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EKG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.92 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: Tris 0.1 M, 2 mM ZnCl2, PEG6000 13% |
-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: Apr 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. obs: 81161 / % possible obs: 99.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.66 / Num. unique all: 4014 / Num. unique obs: 7713 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4zfz Resolution: 1.87→40.17 Å / SU ML: 0.2282 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1495 / 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: 34.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→40.17 Å
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Refine LS restraints |
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LS refinement shell |
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