|Entry||Database: PDB / ID: 7cyd|
|Title||Cryo-EM structures of Alphacoronavirus spike glycoprotein|
|Components||Spike glycoproteinSpike protein|
|Keywords||STRUCTURAL PROTEIN / Alphacoronavirus / spike glycoprotein|
|Function / homology|
Function and homology information
host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / integral component of membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Similarity search - Component
|Biological species||Human coronavirus 229E|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å|
|Authors||Song, X. / Shi, Y. / Ding, W. / Liu, Z.J. / Peng, G.|
|Funding support|| China, 2items |
|Citation||Journal: Nat Commun / Year: 2021|
Title: Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes.
Authors: Xiyong Song / Yuejun Shi / Wei Ding / Tongxin Niu / Limeng Sun / Yubei Tan / Yong Chen / Jiale Shi / Qiqi Xiong / Xiaojun Huang / Shaobo Xiao / Yanping Zhu / Chongyun Cheng / Zhen F Fu / Zhi- ...Authors: Xiyong Song / Yuejun Shi / Wei Ding / Tongxin Niu / Limeng Sun / Yubei Tan / Yong Chen / Jiale Shi / Qiqi Xiong / Xiaojun Huang / Shaobo Xiao / Yanping Zhu / Chongyun Cheng / Zhen F Fu / Zhi-Jie Liu / Guiqing Peng /
Abstract: Coronaviruses spike (S) glycoproteins mediate viral entry into host cells by binding to host receptors. However, how the S1 subunit undergoes conformational changes for receptor recognition has not ...Coronaviruses spike (S) glycoproteins mediate viral entry into host cells by binding to host receptors. However, how the S1 subunit undergoes conformational changes for receptor recognition has not been elucidated in Alphacoronavirus. Here, we report the cryo-EM structures of the HCoV-229E S trimer in prefusion state with two conformations. The activated conformation may pose the potential exposure of the S1-RBDs by decreasing of the interaction area between the S1-RBDs and the surrounding S1-NTDs and S1-RBDs compared to the closed conformation. Furthermore, structural comparison of our structures with the previously reported HCoV-229E S structure showed that the S trimers trended to open the S2 subunit from the closed conformation to open conformation, which could promote the transition from pre- to postfusion. Our results provide insights into the mechanisms involved in S glycoprotein-mediated Alphacoronavirus entry and have implications for vaccine and therapeutic antibody design.
|Structure viewer||Molecule: |
Downloads & links
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
Mass: 122402.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: S, 2
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P15423
Source method: isolated from a genetically manipulated source
Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
|Has ligand of interest||Y|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: HCoV-229E spike trimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT|
|Source (natural)||Organism: Human coronavirus 229E|
|Source (recombinant)||Organism: Insect cell expression vector pTIE1 (others)|
|Buffer solution||pH: 7.2|
|Specimen||Conc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid type: Quantifoil R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|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: 18000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 2000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K / Residual tilt: 5 mradians|
|Image recording||Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Image scans||Scanner model: OTHER|
|Software||Name: PHENIX / Version: 1.18_3855: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 403347|
|3D reconstruction||Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55513 / Symmetry type: POINT|
|Atomic model building||B value: 100 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient|
|Atomic model building||PDB-ID: 5SZS|
Pdb chain-ID: A / Pdb chain residue range: 17-1012
|Refine LS restraints|
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