Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 4877, Year 2022
Publish date	Aug 19, 2022
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 /
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, ...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.
External links	Nat Commun / PubMed:35986008 / PubMed Central
Methods	EM (single particle) / EM (subtomogram averaging)
Resolution	3.1 - 31.0 Å
Structure data	32329 7w6m EMDB-32329, PDB-7w6m: Cryo-EM map of PEDV (Pintung 52) S protein with all three protomers in the D0-down conformation determined in situ on intact viral particles. Method: EM (single particle) / Resolution: 4.7 Å EMDB-32332: Subtomogram averaging of PEDV (Pintung 52) S protein with all three protomers in the D0-down conformation determined in situ on intact viral particles. Method: EM (subtomogram averaging) / Resolution: 19.0 Å EMDB-32333: Subtomogram averaging of PEDV (Pintung 52) S protein with one protomer in the D0-up conformation and two protomers in the D0-down conformation, determined in situ on intact viral particles Method: EM (subtomogram averaging) / Resolution: 27.0 Å EMDB-32337: Subtomogram averaging of PEDV (Pintung 52) S protein with two protomers in the D0-up conformation and one protomer in the D0-down conformation, determined in situ on intact viral particles. Method: EM (subtomogram averaging) / Resolution: 25.0 Å 32338 7w73 EMDB-32338, PDB-7w73: Cryo-EM map of PEDV S protein with one protomer in the D0-up conformation while the other two in the D0-down conformation Method: EM (single particle) / Resolution: 6.4 Å EMDB-32339: Subtomogram averaging of PEDV (Pintung 52) S protein with all three protomers in the D0-up conformation determined in situ on intact viral particles. Method: EM (subtomogram averaging) / Resolution: 29.0 Å EMDB-32340: Subtomogram averaging of PEDV (Pintung 52) S protein in the postfusion form determined in situ on intact viral particles. Method: EM (subtomogram averaging) / Resolution: 31.0 Å 33646 7y6s EMDB-33646, PDB-7y6s: Cryo-EM map of IPEC-J2 cell-derived PEDV PT52 S protein with three D0-up Method: EM (single particle) / Resolution: 3.1 Å 33647 7y6t EMDB-33647, PDB-7y6t: Cryo-EM map of IPEC-J2 cell-derived PEDV PT52 S protein one D0-down and two D0-up Method: EM (single particle) / Resolution: 4.2 Å 33648 7y6u EMDB-33648, PDB-7y6u: Symmetry-expanded and locally refined protomer structure of IPEC-J2 cell-derived PEDV PT52 S with a CTD-close conformation Method: EM (single particle) / Resolution: 3.2 Å 33649 7y6v EMDB-33649, PDB-7y6v: Symmetry-expanded and locally refined protomer structure of IPEC-J2 cell-derived PEDV PT52 S with a CTD-open conformation Method: EM (single particle) / Resolution: 3.3 Å EMDB-33700: Cryo-EM map of HEK293F cell-derived PEDV PT52 S protein with three D0-down Method: EM (single particle) / Resolution: 5.6 Å EMDB-33701: Cryo-EM map of HEK293F cell-derived PEDV PT52 S protein one D0-up and two D0-down Method: EM (single particle) / Resolution: 10.2 Å EMDB-33702: Cryo-EM map of HEK293F cell-derived PEDV PT52 S protein with three D0-up Method: EM (single particle) / Resolution: 4.5 Å EMDB-33703: Cryo-EM map of HEK293F cell-derived PEDV PT52 S T326I with three D0-down Method: EM (single particle) / Resolution: 5.2 Å EMDB-33704: Cryo-EM map of HEK293F cell-derived PEDV PT52 S T326I one D0-up and two D0-down Method: EM (single particle) / Resolution: 8.0 Å EMDB-33705: Cryo-EM map of HEK293F cell-derived PEDV PT52 S T326I one D0-down and two D0-up Method: EM (single particle) / Resolution: 6.1 Å EMDB-33706: Cryo-EM map of HEK293F cell-derived PEDV PT52 S T326I with three D0-up Method: EM (single particle) / Resolution: 6.2 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine
Source	porcine epidemic diarrhea virus
Keywords	VIRAL PROTEIN / PEDV / Spike / Glycoprotein