[English] 日本語
Yorodumi- PDB-6j2e: Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j2e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Ebola virus-derived peptide EBOV-NP1 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information viral RNA genome packaging / helical viral capsid / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...viral RNA genome packaging / helical viral capsid / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / sensory perception of smell / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / immune response / ribonucleoprotein complex / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Pteropus alecto (black flying fox) Homo sapiens (human) Ebola virus sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lu, D. / Liu, K.F. / Yue, C. / Lu, Q. / Cheng, H. / Chai, Y. / Qi, J.X. / Gao, G.F. / Liu, W.J. | ||||||
Citation | Journal: Plos Biol. / Year: 2019 Title: Peptide presentation by bat MHC class I provides new insight into the antiviral immunity of bats. Authors: Lu, D. / Liu, K. / Zhang, D. / Yue, C. / Lu, Q. / Cheng, H. / Wang, L. / Chai, Y. / Qi, J. / Wang, L.F. / Gao, G.F. / Liu, W.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6j2e.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6j2e.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 6j2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j2e_validation.pdf.gz | 460.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6j2e_full_validation.pdf.gz | 469.4 KB | Display | |
Data in XML | 6j2e_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 6j2e_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/6j2e ftp://data.pdbj.org/pub/pdb/validation_reports/j2/6j2e | HTTPS FTP |
-Related structure data
Related structure data | 6j2dC 6j2fC 6j2gC 6j2hC 6j2iC 6j2jC 6k7tC 6k7uC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32119.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: Ptal-N / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A125R585 #2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P61769 #3: Protein/peptide | Mass: 1158.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Ebola virus sp. / References: UniProt: O72142*PLUS #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.73 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M succinic acid pH 7.0, 15%(w/v) polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å |
Detector | Type: SDMS / Detector: IMAGE PLATE / Date: Aug 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 54243 / % possible obs: 100 % / Redundancy: 9.9 % / Net I/σ(I): 2.365 |
Reflection shell | Resolution: 2.1→2.18 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.284 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 26.75
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.284 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|