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- PDB-8hr0: The complex structure of COPII coat with HCoV-OC43 DD sorting motif -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hr0 | ||||||
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Title | The complex structure of COPII coat with HCoV-OC43 DD sorting motif | ||||||
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![]() | TRANSPORT PROTEIN / HCoV-OC43 / Spike / COPII vesicle / DD sorting motif | ||||||
Function / homology | ![]() vesicle fusion with Golgi apparatus / regulation of cholesterol transport / COPII-coated vesicle cargo loading / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...vesicle fusion with Golgi apparatus / regulation of cholesterol transport / COPII-coated vesicle cargo loading / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum exit site / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / protein localization to plasma membrane / cholesterol homeostasis / positive regulation of protein secretion / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / positive regulation of protein catabolic process / phagocytic vesicle membrane / melanosome / protein transport / ER-Phagosome pathway / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, W.F. / Nan, Y.N. / Yang, M.R. / Li, Y.Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tighter ER retention of SARS-CoV-2 Omicron spike caused by a constellation of folding disruptive mutations Authors: Li, Y.Q. / Yang, M.R. / Nan, Y.N. / Wang, J.M. / Guo, J.J. / He, P.F. / Dai, W.X. / Zhou, S.Q. / Wang, S.J. / Zhang, Y. / Ma, W.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327.3 KB | Display | ![]() |
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PDB format | ![]() | 254.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.7 KB | Display | ![]() |
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Full document | ![]() | 529.9 KB | Display | |
Data in XML | ![]() | 59.9 KB | Display | |
Data in CIF | ![]() | 80.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hqtC ![]() 8hqvC ![]() 8hqwC 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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Unit cell |
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Components
#1: Protein | Mass: 86249.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q15436 | ||
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#2: Protein | Mass: 84761.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O95486 | ||
#3: Protein | Mass: 22683.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#4: Protein/peptide | Mass: 1158.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
#5: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 281.15 K / Method: evaporation / Details: 50 mM Tris-HCl, pH 7.9, 0.2 M NaAc and 16% PEG4000 |
-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: Sep 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.34→50 Å / Num. obs: 26475 / % possible obs: 98.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 3.34→3.45 Å / Num. unique obs: 2430 / CC1/2: 0.716 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.34→49.023 Å
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Refine LS restraints |
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LS refinement shell |
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