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Yorodumi- PDB-6vv5: Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vv5 | ||||||||||||
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Title | Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein | ||||||||||||
Components | Spike glycoprotein | ||||||||||||
Keywords | VIRAL PROTEIN / glycoprotein / surface / receptor-binding / membrane fusion | ||||||||||||
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 | Porcine epidemic diarrhea virus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Kirchdoerfer, R.N. / Ward, A.B. | ||||||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2021 Title: Structure and immune recognition of the porcine epidemic diarrhea virus spike protein. Authors: Robert N Kirchdoerfer / Mahesh Bhandari / Olnita Martini / Leigh M Sewall / Sandhya Bangaru / Kyoung-Jin Yoon / Andrew B Ward / Abstract: Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a ...Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components, including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins. | ||||||||||||
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 | 6vv5.cif.gz | 671.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vv5.ent.gz | 557 KB | Display | PDB format |
PDBx/mmJSON format | 6vv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vv5_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6vv5_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6vv5_validation.xml.gz | 100.6 KB | Display | |
Data in CIF | 6vv5_validation.cif.gz | 152.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/6vv5 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/6vv5 | HTTPS FTP |
-Related structure data
Related structure data | 21391MC 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 / Non-polymers , 2 types, 9 molecules ABC
#1: Protein | Mass: 148463.656 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine epidemic diarrhea virus / Variant: 13-019349 / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S5RJN4 #6: Chemical | ChemComp-PAM / |
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-Sugars , 4 types, 45 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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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: Porcine epidemic diarrhea virus spike protein / Type: COMPLEX Details: Recombinantly expressed in insect cells using a baculovirus vector. Entity ID: #1 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 0.6 MDa / Experimental value: YES | ||||||||||||
Source (natural) | Organism: Porcine epidemic diarrhea virus / Strain: 13-019349 | ||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9 | ||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||
Buffer component |
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Specimen | Conc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 600 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K |
Image recording | Average exposure time: 12.8 sec. / Electron dose: 54.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Movie frames/image: 64 / Used frames/image: 1-64 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 19436 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19436 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5SZS Pdb chain-ID: A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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