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- PDB-6iwh: 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: 6iwh | |||||||||||||||
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Title | Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with C14-GGGI lipopeptide | |||||||||||||||
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![]() | IMMUNE SYSTEM / antigen presentation / major histocompatibility complex / N-myristoylation / AIDS / Nef | |||||||||||||||
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 | ![]() ![]() ![]() | |||||||||||||||
![]() | Yamamoto, Y. / Morita, D. / Sugita, M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Identification and Structure of an MHC Class I-Encoded Protein with the Potential to PresentN-Myristoylated 4-mer Peptides to T Cells. Authors: Yamamoto, Y. / Morita, D. / Shima, Y. / Midorikawa, A. / Mizutani, T. / Suzuki, J. / Mori, N. / Shiina, T. / Inoko, H. / 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 | ![]() | 184.5 KB | Display | ![]() |
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PDB format | ![]() | 143.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.8 KB | Display | ![]() |
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Full document | ![]() | 456.8 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iwgC ![]() 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31919.098 Da / Num. of mol.: 1 / Mutation: R128E,K177E,D223E,K264E 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.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 512.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 272 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM Sodium fluoride, 100mM Bis-Tris propane, 20% PEG 3350 |
-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: Jul 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 35329 / % possible obs: 99.8 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 46 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.262 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZFZ Resolution: 1.95→44.4 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.95→44.4 Å
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LS refinement shell | Resolution: 1.95→2 Å
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