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Open data
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Basic information
Entry | Database: PDB / ID: 7xqs | ||||||
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Title | The structure of FLA-K*00701/KP-CoV-9 | ||||||
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![]() | IMMUNE SYSTEM / Complex / Peptide prensentation / STRUCTURAL PROTEIN | ||||||
Function / homology | ![]() 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 / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / immune response / lysosomal membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.4 KB | Display | ![]() |
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Full document | ![]() | 460.9 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xqtC ![]() 7xquC ![]() 5xmfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 13714.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1140.309 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: P0DTC2 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.16 % |
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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: ![]() ![]() ![]() |
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: 2.69→61.17 Å / Num. obs: 13627 / % possible obs: 99.2 % / Redundancy: 12.8 % / Biso Wilson estimate: 79.62 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.69→2.83 Å / Rmerge(I) obs: 0.857 / Num. unique obs: 13627 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XMF Resolution: 2.69→27.89 Å / SU ML: 0.3939 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 34.0884 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→27.89 Å
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Refine LS restraints |
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LS refinement shell |
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