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Yorodumi- PDB-7y6v: Symmetry-expanded and locally refined protomer structure of IPEC-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y6v | |||||||||||||||||||||
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Title | Symmetry-expanded and locally refined protomer structure of IPEC-J2 cell-derived PEDV PT52 S with a CTD-open conformation | |||||||||||||||||||||
Components | Spike glycoproteinSpike protein | |||||||||||||||||||||
Keywords | VIRAL PROTEIN / PEDV / Spike / Glycoprotein | |||||||||||||||||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / 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 / membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Porcine epidemic diarrhea virus | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||
Authors | Hsu, S.T.D. / Draczkowski, P. / Wang, Y.S. | |||||||||||||||||||||
Funding support | Taiwan, 6items
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Citation | Journal: Nat Commun / Year: 2022 Title: In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM. Authors: Cheng-Yu Huang / Piotr Draczkowski / Yong-Sheng Wang / Chia-Yu Chang / Yu-Chun Chien / Yun-Han Cheng / Yi-Min Wu / Chun-Hsiung Wang / Yuan-Chih Chang / Yen-Chen Chang / Tzu-Jing Yang / Yu-Xi ...Authors: Cheng-Yu Huang / Piotr Draczkowski / Yong-Sheng Wang / Chia-Yu Chang / Yu-Chun Chien / Yun-Han Cheng / Yi-Min Wu / Chun-Hsiung Wang / Yuan-Chih Chang / Yen-Chen Chang / Tzu-Jing Yang / Yu-Xi Tsai / Kay-Hooi Khoo / Hui-Wen Chang / Shang-Te Danny Hsu / Abstract: Porcine epidemic diarrhea (PED) is a highly contagious swine disease caused by porcine epidemic diarrhea virus (PEDV). PED causes enteric disorders with an exceptionally high fatality in neonates, ...Porcine epidemic diarrhea (PED) is a highly contagious swine disease caused by porcine epidemic diarrhea virus (PEDV). PED causes enteric disorders with an exceptionally high fatality in neonates, bringing substantial economic losses in the pork industry. The trimeric spike (S) glycoprotein of PEDV is responsible for virus-host recognition, membrane fusion, and is the main target for vaccine development and antigenic analysis. The atomic structures of the recombinant PEDV S proteins of two different strains have been reported, but they reveal distinct N-terminal domain 0 (D0) architectures that may correspond to different functional states. The existence of the D0 is a unique feature of alphacoronavirus. Here we combined cryo-electron tomography (cryo-ET) and cryo-electron microscopy (cryo-EM) to demonstrate in situ the asynchronous S protein D0 motions on intact viral particles of a highly virulent PEDV Pintung 52 strain. We further determined the cryo-EM structure of the recombinant S protein derived from a porcine cell line, which revealed additional domain motions likely associated with receptor binding. By integrating mass spectrometry and cryo-EM, we delineated the complex compositions and spatial distribution of the PEDV S protein N-glycans, and demonstrated the functional role of a key N-glycan in modulating the D0 conformation. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y6v.cif.gz | 239.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y6v.ent.gz | 189.2 KB | Display | PDB format |
PDBx/mmJSON format | 7y6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/7y6v ftp://data.pdbj.org/pub/pdb/validation_reports/y6/7y6v | HTTPS FTP |
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-Related structure data
Related structure data | 33649MC 7w6mC 7w73C 7y6sC 7y6tC 7y6uC M: map data used to model this data 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 153739.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine epidemic diarrhea virus / Production host: Sus scrofa (pig) / References: UniProt: A0A1Y0DD46 |
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-Sugars , 7 types, 21 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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 | ||||||||
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: 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 #6: 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 #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | Y |
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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: recombinant Porcine epidemic diarrhea virus (strain Pintung 52) 2P Spike Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Porcine epidemic diarrhea virus / Strain: Pintung 52 | ||||||||||||||||||||
Source (recombinant) | Organism: Sus scrofa (pig) / Cell: IPEC-J2 | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Sus scrofa | ||||||||||||||||||||
Buffer solution | pH: 7.6 / Details: Blot for 3 seconds before plunging. Force 0. | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Symmetry-expanded and locally refined protomer structure of IPEC-J2 cell-derived PEDV PT52 S with a CTD-open conformation | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 64000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 55.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3701 |
EM imaging optics | Energyfilter name: GIF Bioquantum |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 337583 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124142 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 148.87 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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