+Open data
-Basic information
Entry | Database: PDB / ID: 7xqt | ||||||
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Title | The structure of FLA-K*00701/KP-FECV-11 | ||||||
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 / endocytosis involved in viral entry into host cell / 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 ...antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / lumenal side of endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell / 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 membrane / receptor-mediated virion attachment to host cell / immune response / lysosomal membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Felis catus (domestic cat) Feline coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 7xqt.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xqt.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xqt_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 7xqt_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 7xqt_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 7xqt_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xqt ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xqt | HTTPS FTP |
-Related structure data
Related structure data | 7xqsC 7xquC 5xfmS 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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Unit cell |
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-Components
#1: Protein | Mass: 31467.830 Da / Num. of mol.: 1 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: C6ZK69 |
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#2: Protein | Mass: 11618.078 Da / Num. of mol.: 1 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: 1050.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Feline coronavirus / References: UniProt: A0A125R5A5 |
#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: 2.56 Å3/Da / Density % sol: 51.86 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Sodium chloride, 0.1M HEPES PH 7, 25% (W/V) SOKALAN PA 25 CL |
-Data collection
Diffraction | Mean temperature: 100 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: Jul 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60.84 Å / Num. obs: 11706 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 62.81 Å2 / Rmerge(I) obs: 0.277 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Rmerge(I) obs: 1.45 / Num. unique obs: 11706 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XFM Resolution: 2.8→45.57 Å / SU ML: 0.5667 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4969 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: 63.21 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.57 Å
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Refine LS restraints |
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LS refinement shell |
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