|Entry||Database: PDB / ID: 5x58|
|Title||Prefusion structure of SARS-CoV spike glycoprotein, conformation 1|
|Keywords||VIRAL PROTEIN / SARS-CoV / spike glycoprotein / prefusion / single particle|
|Function / homology|
Function and homology information
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 / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / pathogenesis ...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 / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / pathogenesis / integral component of membrane / identical protein binding
Spike glycoprotein N-terminal domain / Spike receptor binding domain superfamily / Spike receptor binding domain / Spike glycoprotein / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal
|Biological species||SARS coronavirus BJ01|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å|
|Authors||Yuan, Y. / Cao, D. / Zhang, Y. / Ma, J. / Qi, J. / Wang, Q. / Lu, G. / Wu, Y. / Yan, J. / Shi, Y. / Zhang, X. / Gao, G.F.|
|Funding support|| China, 11items |
|Citation||Journal: Nat Commun / Year: 2017|
Title: Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.
Authors: Yuan Yuan / Duanfang Cao / Yanfang Zhang / Jun Ma / Jianxun Qi / Qihui Wang / Guangwen Lu / Ying Wu / Jinghua Yan / Yi Shi / Xinzheng Zhang / George F Gao /
Abstract: The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and ...The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
Mass: 136825.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus BJ01 / Strain: BJ01 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594*PLUS
Mass: 221.208 Da / Num. of mol.: 42
Source method: isolated from a genetically manipulated source
|Sequence details||THE REFERENCE SEQUENCE DATABASE OF THIS PROTEIN IS RESIDUES 14-1193 IN GENBANK AAP30030.1. RESIDUES ...THE REFERENCE SEQUENCE DATABASE OF THIS PROTEIN IS RESIDUES 14-1193 IN GENBANK AAP30030.1. RESIDUES 1194-1241 ARE EXPRESSION|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: SARS-CoV spike trimer / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: SARS coronavirus BJ01 / Strain: BJ01|
|Source (recombinant)||Organism: Spodoptera frugiperda (fall armyworm)|
|Buffer solution||pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-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|
|Image recording||Electron dose: 8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Software||Name: PHENIX / Version: dev_2411: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60000 / Symmetry type: POINT|
|Atomic model building||Protocol: RIGID BODY FIT|
|Atomic model building|
|Refine LS restraints|
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