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Yorodumi- PDB-6irl: Crystal structure of 8-mer peptide from avian influenza H5N1 viru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6irl | ||||||
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Title | Crystal structure of 8-mer peptide from avian influenza H5N1 virus in complex with BF2*1501 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class I / Chicken / Avian influenza virus / H5N1 / epitope / 8-mer | ||||||
Function / homology | Function and homology information ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Neutrophil degranulation / 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 ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Neutrophil degranulation / 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / 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 / protein homotetramerization / endonuclease activity / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / Hydrolases; Acting on ester bonds / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / viral RNA genome replication / signaling receptor binding / DNA-templated transcription / host cell nucleus / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / extracellular region / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Xiao, L. / Zhang, L. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structures of the MHC-I molecule BF2*1501 disclose the preferred presentation of an H5N1 virus-derived epitope. Authors: Li, X. / Zhang, L. / Liu, Y. / Ma, L. / Zhang, N. / Xia, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6irl.cif.gz | 179.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6irl.ent.gz | 140 KB | Display | PDB format |
PDBx/mmJSON format | 6irl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6irl_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 6irl_full_validation.pdf.gz | 455.8 KB | Display | |
Data in XML | 6irl_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 6irl_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/6irl ftp://data.pdbj.org/pub/pdb/validation_reports/ir/6irl | HTTPS FTP |
-Related structure data
Related structure data | 6kx9C 4e0rS 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
#1: Protein | Mass: 31065.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: BF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GIP6 |
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#2: Protein | Mass: 11469.888 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P21611 |
#3: Protein/peptide | Mass: 1126.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q809J3 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.33 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.1M BIS-TRIS pH6.5, 0.2M Sodium chloride, 1.5M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.54178 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Jan 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.112 / Net I/σ(I): 20.072 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 6.477 / Num. unique obs: 165438 / Rsym value: 0.343 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E0R Resolution: 2.1→25.176 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 18.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.281 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→25.176 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -14.5976 Å / Origin y: 1.8761 Å / Origin z: -3.6307 Å
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Refinement TLS group | Selection details: all |