7Y6U

Symmetry-expanded and locally refined protomer structure of IPEC-J2 cell-derived PEDV PT52 S with a CTD-close conformation

Summary for 7Y6U

• Entry DOI: 10.2210/pdb7y6u/pdb
• EMDB information: 33648
• Descriptor: Spike glycoprotein, 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, 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, ... (7 entities in total)
• Functional Keywords: pedv, spike, glycoprotein, viral protein
• Biological source: Porcine epidemic diarrhea virus
• Total number of polymer chains: 1
• Total formula weight: 161593.94

Authors

Hsu, S.T.D.,Draczkowski, P.,Wang, Y.S. (deposition date: 2022-06-21, release date: 2022-08-03, Last modification date: 2022-09-14)

Primary citation

Huang, C.Y.,Draczkowski, P.,Wang, Y.S.,Chang, C.Y.,Chien, Y.C.,Cheng, Y.H.,Wu, Y.M.,Wang, C.H.,Chang, Y.C.,Chang, Y.C.,Yang, T.J.,Tsai, Y.X.,Khoo, K.H.,Chang, H.W.,Hsu, S.D.
In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM.
Nat Commun, 13:4877-4877, 2022

PubMed 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, 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.

PubMed: 35986008
DOI: 10.1038/s41467-022-32588-3

Experimental method

ELECTRON MICROSCOPY (3.2 Å)