|Entry||Database: EMDB / ID: EMD-30660|
|Title||SARS-CoV-2 S trimer, S-closed|
|Sample||SARS-CoV-2 spike glycoprotein trimer:|
Spike glycoproteinPeplomer / ligand
|Function / homology|
Function and homology information
suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope ...suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike glycoprotein S2, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal
|Biological species||Severe acute respiratory syndrome coronavirus 2|
|Method||single particle reconstruction / cryo EM / Resolution: 2.7 Å|
|Authors||Cong X / Yao C|
|Funding support|| China, 1 items |
|Citation||Journal: Sci Adv / Year: 2021|
Title: Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM.
Authors: Cong Xu / Yanxing Wang / Caixuan Liu / Chao Zhang / Wenyu Han / Xiaoyu Hong / Yifan Wang / Qin Hong / Shutian Wang / Qiaoyu Zhao / Yalei Wang / Yong Yang / Kaijian Chen / Wei Zheng / ...Authors: Cong Xu / Yanxing Wang / Caixuan Liu / Chao Zhang / Wenyu Han / Xiaoyu Hong / Yifan Wang / Qin Hong / Shutian Wang / Qiaoyu Zhao / Yalei Wang / Yong Yang / Kaijian Chen / Wei Zheng / Liangliang Kong / Fangfang Wang / Qinyu Zuo / Zhong Huang / Yao Cong /
Abstract: The recent outbreaks of SARS-CoV-2 pose a global health emergency. The SARS-CoV-2 trimeric spike (S) glycoprotein interacts with the human ACE2 receptor to mediate viral entry into host cells. We ...The recent outbreaks of SARS-CoV-2 pose a global health emergency. The SARS-CoV-2 trimeric spike (S) glycoprotein interacts with the human ACE2 receptor to mediate viral entry into host cells. We report the cryo-EM structures of a tightly closed SARS-CoV-2 S trimer with packed fusion peptide and an ACE2-bound S trimer at 2.7- and 3.8-Å resolution, respectively. Accompanying ACE2 binding to the up receptor-binding domain (RBD), the associated ACE2-RBD exhibits continuous swing motions. Notably, the SARS-CoV-2 S trimer appears much more sensitive to the ACE2 receptor than the SARS-CoV S trimer regarding receptor-triggered transformation from the closed prefusion state to the fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2. Our findings depict the mechanism of ACE2-induced S trimer conformational transitions from the ground prefusion state toward the postfusion state, facilitating development of anti-SARS-CoV-2 vaccines and therapeutics.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_30660.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.02 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Additional map: S-closed map before post-processing
-Entire SARS-CoV-2 spike glycoprotein trimer
|Entire||Name: SARS-CoV-2 spike glycoprotein trimer / Number of components: 3|
-Component #1: protein, SARS-CoV-2 spike glycoprotein trimer
|Protein||Name: SARS-CoV-2 spike glycoprotein trimer / Recombinant expression: No|
|Source||Species: Severe acute respiratory syndrome coronavirus 2|
|Source (engineered)||Expression System: Homo sapiens (human) / Strain: HEK293F|
-Component #2: protein, Spike glycoprotein
|Protein||Name: Spike glycoproteinPeplomer / Number of Copies: 3 / Recombinant expression: No|
|Mass||Theoretical: 140.055906 kDa|
|Source||Species: Severe acute respiratory syndrome coronavirus 2|
|Source (engineered)||Expression System: Homo sapiens (human)|
-Component #3: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose
|Ligand||Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 30 / Recombinant expression: No|
|Mass||Theoretical: 0.221208 kDa|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|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: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 142345|
|3D reconstruction||Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-Aug 12, 2020. New: Covid-19 info
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-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
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