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Yorodumi- PDB-6iwg: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*0... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iwg | |||||||||||||||
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Title | Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein | |||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Antigen presentation / Major histocompatibility complex / N-myristoylation / AIDS / nef | |||||||||||||||
Function / homology | Function and homology information 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 | Macaca mulatta (Rhesus monkey) Simian immunodeficiency virus | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||||||||
Authors | Yamamoto, Y. / Morita, D. / Sugita, M. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: J Immunol. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iwg.cif.gz | 189.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iwg.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 6iwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iwg_validation.pdf.gz | 478.1 KB | Display | wwPDB validaton report |
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Full document | 6iwg_full_validation.pdf.gz | 480.6 KB | Display | |
Data in XML | 6iwg_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 6iwg_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/6iwg ftp://data.pdbj.org/pub/pdb/validation_reports/iw/6iwg | HTTPS FTP |
-Related structure data
Related structure data | 6iwhC 4zfzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Macaca mulatta (Rhesus monkey) / Gene: Mamu-B*05104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: B2ZHY7 |
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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.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q6V7J5 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 526.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus |
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-Non-polymers , 4 types, 329 molecules
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.68 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM MIB, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 44246 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 43.9 |
Reflection shell | Resolution: 1.8→1.84 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZFZ Resolution: 1.8→44.7 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.8→44.7 Å
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