In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM

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 and Shang-Te Danny Hsu ()
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Cheng-Yu Huang: Institute of Biological Chemistry, Academia Sinica
Piotr Draczkowski: Institute of Biological Chemistry, Academia Sinica
Yong-Sheng Wang: Institute of Biological Chemistry, Academia Sinica
Chia-Yu Chang: Institute of Biological Chemistry, Academia Sinica
Yu-Chun Chien: Institute of Biological Chemistry, Academia Sinica
Yun-Han Cheng: National Taiwan University
Yi-Min Wu: Academia Sinica Cryo-EM Center, Academia Sinica
Chun-Hsiung Wang: Academia Sinica Cryo-EM Center, Academia Sinica
Yuan-Chih Chang: Institute of Biological Chemistry, Academia Sinica
Yen-Chen Chang: National Taiwan University
Tzu-Jing Yang: Institute of Biological Chemistry, Academia Sinica
Yu-Xi Tsai: Institute of Biological Chemistry, Academia Sinica
Kay-Hooi Khoo: Institute of Biological Chemistry, Academia Sinica
Hui-Wen Chang: National Taiwan University
Shang-Te Danny Hsu: Institute of Biological Chemistry, Academia Sinica

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-32588-3

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