+Open data
-Basic information
Entry | Database: PDB / ID: 7xqu | ||||||
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Title | The structure of FLA-E*00301/EM-FECV-10 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complex / Peptide prensentation / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response ...antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / immune response / lysosomal membrane / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Felis catus (domestic cat) Feline coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Qiao, P.W. / Yue, C. / Peng, W.Y. / Liu, K.F. / Huo, S.T. / Zhang, D. / Chai, Y. / Qi, J.X. / Sun, Z.Y. / Gao, G.F. ...Qiao, P.W. / Yue, C. / Peng, W.Y. / Liu, K.F. / Huo, S.T. / Zhang, D. / Chai, Y. / Qi, J.X. / Sun, Z.Y. / Gao, G.F. / Liu, W.J. / Wu, G.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Analysis of the characteristics of feline major histocompatibility complex class I molecules cross-presenting coronavirus peptides Authors: Qiao, P.W. / Yue, C. / Peng, W.Y. / Liu, K.F. / Huo, S.T. / Zhang, D. / Chai, Y. / Qi, J.X. / Sun, Z.Y. / Gao, G.F. / Liu, W.J. / Wu, G.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xqu.cif.gz | 203.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xqu.ent.gz | 131.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xqu ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xqu | HTTPS FTP |
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-Related structure data
Related structure data | 7xqsC 7xqtC 5xmfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31878.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Felis catus (domestic cat) / Gene: FLA-I / Production host: Escherichia coli (E. coli) / References: UniProt: Q95482 #2: Protein | Mass: 11618.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Felis catus (domestic cat) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MGS7 #3: Protein/peptide | Mass: 1127.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Feline coronavirus / References: UniProt: P25909 #4: 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: 3.21 Å3/Da / Density % sol: 61.64 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES sodium, 2% VL Polyethylene glycol 400, 2.0M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 35453 / % possible obs: 97.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 45.86 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.909 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.669 / Num. unique obs: 35453 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XMF Resolution: 2.6→38.04 Å / SU ML: 0.3884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0358 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.04 Å
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Refine LS restraints |
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LS refinement shell |
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