|Entry||Database: EMDB / ID: 7063|
|Title||Cryo-electron microscopy structure of porcine delta coronavirus spike protein in the pre-fusion state|
|Map data||Delta coronavirus spike protein in the pre-fusion state|
|Sample||Porcine delta coronavirus spike trimer in the pre-fusion state:|
Spike protein / ligand
|Function / homology||Coronavirus S1 glycoprotein / Coronavirus S2 glycoprotein / Coronavirus S1 glycoprotein / Coronavirus S2 glycoprotein / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / integral component of membrane / Spike protein / Spike protein|
Function and homology information
|Method||single particle reconstruction / cryo EM / 3.3 Å resolution|
|Authors||Shang J / Zheng Y / Yang Y / Liu C / Geng Q / Tai W / Du L / Zhou Y / Zhang W / Li F|
|Citation||Journal: J. Virol. / Year: 2017|
Title: Cryo-EM structure of porcine delta coronavirus spike protein in the pre-fusion state.
Authors: Jian Shang / Yuan Zheng / Yang Yang / Chang Liu / Qibin Geng / Wanbo Tai / Lanying Du / Yusen Zhou / Wei Zhang / Fang Li
Abstract: Coronavirus spike proteins from different genera are divergent, although they all mediate coronavirus entry into cells by binding to host receptors and fusing viral and cell membranes. Here we ...Coronavirus spike proteins from different genera are divergent, although they all mediate coronavirus entry into cells by binding to host receptors and fusing viral and cell membranes. Here we determined the cryo-EM structure of porcine delta coronavirus (PdCoV) spike protein at 3.3-angstrom resolution. The trimeric protein contains three receptor-binding S1 subunits that tightly pack into a crown-like structure and three membrane-fusion S2 subunits that form a stalk. Each S1 subunit contains two domains, N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD). PdCoV S1-NTD has the same structural fold as alpha- and beta-coronavirus S1-NTDs as well as host galectins, and it recognizes sugar as its potential receptor. PdCoV S1-CTD has the same structural fold as alpha-coronavirus S1-CTDs, but its structure differs from that of beta-coronavirus S1-CTDs. PdCoV S1-CTD binds to an unidentified receptor on host cell surfaces. PdCoV S2 is locked in the pre-fusion conformation by structural restraint of S1 from a different monomeric subunit. PdCoV spike possesses several structural features that may facilitate immune evasion by the virus, such as its compact structure, concealed receptor-binding sites, and shielded critical epitopes. Overall, this study reveals that delta-coronavirus spikes are structurally and evolutionally more closely related to alpha-coronavirus spikes than to beta-coronavirus spikes; it also has implications for the receptor recognition, membrane fusion, and immune evasion by delta-coronaviruses as well as coronaviruses in general. In this study we determined the cryo-EM structure of porcine delta coronavirus (PdCoV) spike protein at 3.3 angstrom. This is the first atomic structure of a spike protein from the delta coronavirus genus, which is divergent in amino acid sequences from the well-studied alpha- and beta-coronavirus spike proteins. In the current study, we described the overall structure of the PdCoV spike and the detailed structure of each of its structural elements. Moreover, we analyzed the functions of each of the structural elements. Based on the structures and functions of these structural elements, we discussed the evolution of PdCoV spike protein in relation to the spike proteins from other coronavirus genera. This study combines the structure, function, and evolution of coronavirus spike proteins, and provides many insights into the receptor recognition, membrane fusion, immune evasion, and evolution of PdCoV spike protein.
|Validation Report||PDB-ID: 6b7n|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 4, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Oct 25, 2017 / Last update: Dec 6, 2017|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7063.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.3 Å|
CCP4 map header:
-Entire Porcine delta coronavirus spike trimer in the pre-fusion state
|Entire||Name: Porcine delta coronavirus spike trimer in the pre-fusion state|
Number of components: 3
-Component #1: protein, Porcine delta coronavirus spike trimer in the pre-fusion...
|Protein||Name: Porcine delta coronavirus spike trimer in the pre-fusion state|
Recombinant expression: No
|Source||Species: Deltacoronavirus PDCoV/USA/Ohio137/2014|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm)|
-Component #2: protein, Spike protein
|Protein||Name: Spike protein / Recombinant expression: No|
|Mass||Theoretical: 122.277266 kDa|
|Source (engineered)||Expression System: Deltacoronavirus PDCoV/USA/Ohio137/2014|
-Component #3: ligand, N-ACETYL-D-GLUCOSAMINE
|Ligand||Name: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 57 / Recombinant expression: No|
|Mass||Theoretical: 0.221208 kDa|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.35 mg/ml / pH: 7.2|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 87002|
|3D reconstruction||Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF|
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