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Yorodumi- PDB-6jx7: Cryo-EM structure of spike protein of feline infectious peritonit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jx7 | ||||||||||||
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Title | Cryo-EM structure of spike protein of feline infectious peritonitis virus strain UU4 | ||||||||||||
Components | Feline Infectious Peritonitis Virus Spike Protein | ||||||||||||
Keywords | VIRAL PROTEIN / CoV spike protein | ||||||||||||
Function / homology | Function and homology information : / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane Similarity search - Function | ||||||||||||
Biological species | Feline infectious peritonitis virus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å | ||||||||||||
Authors | Hsu, S.T.D. / Yang, T.J. / Ko, T.P. / Draczkowski, P. | ||||||||||||
Funding support | Taiwan, 3items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans. Authors: Tzu-Jing Yang / Yen-Chen Chang / Tzu-Ping Ko / Piotr Draczkowski / Yu-Chun Chien / Yuan-Chih Chang / Kuen-Phon Wu / Kay-Hooi Khoo / Hui-Wen Chang / Shang-Te Danny Hsu / Abstract: Feline infectious peritonitis virus (FIPV) is an alphacoronavirus that causes a nearly 100% mortality rate without effective treatment. Here we report a 3.3-Å cryoelectron microscopy (cryo-EM) ...Feline infectious peritonitis virus (FIPV) is an alphacoronavirus that causes a nearly 100% mortality rate without effective treatment. Here we report a 3.3-Å cryoelectron microscopy (cryo-EM) structure of the serotype I FIPV spike (S) protein, which is responsible for host recognition and viral entry. Mass spectrometry provided site-specific compositions of densely distributed high-mannose and complex-type Nglycans that account for 1/4 of the total molecular mass; most of the N-glycans could be visualized by cryo-EM. Specifically, the N-glycans that wedge between 2 galectin-like domains within the S1 subunit of FIPV S protein result in a unique propeller-like conformation, underscoring the importance of glycosylation in maintaining protein structures. The cleavage site within the S2 subunit responsible for activation also showed distinct structural features and glycosylation. These structural insights provide a blueprint for a better molecular understanding of the pathogenesis of FIP. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jx7.cif.gz | 715.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jx7.ent.gz | 598.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jx7_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 6jx7_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 6jx7_validation.xml.gz | 115.9 KB | Display | |
Data in CIF | 6jx7_validation.cif.gz | 169.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/6jx7 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/6jx7 | HTTPS FTP |
-Related structure data
Related structure data | 9891MC M: map data used to model this data 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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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 163829.844 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Feline infectious peritonitis virus / Production host: Homo sapiens (human) / References: UniProt: C6GHB7*PLUS |
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-Sugars , 9 types, 87 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / #10: Sugar | ChemComp-MAN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Feline Infectious Peritonitis Virus Spike Protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 720 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Feline infectious peritonitis virus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 / Details: 1X D-PBS |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: blot for 3 seconds before plunging; blot force: 0; waiting time: 10s |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 1.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2436 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 442004 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102586 / Symmetry type: POINT |