6X2C

SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer

  • Classification: VIRAL PROTEIN
  • Organism(s): Severe acute respiratory syndrome coronavirus 2
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2020-05-20 Released: 2020-05-27 
  • Deposition Author(s): Henderson, R., Acharya, P.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Controlling the SARS-CoV-2 spike glycoprotein conformation.

Henderson, R.Edwards, R.J.Mansouri, K.Janowska, K.Stalls, V.Gobeil, S.M.C.Kopp, M.Li, D.Parks, R.Hsu, A.L.Borgnia, M.J.Haynes, B.F.Acharya, P.

(2020) Nat Struct Mol Biol 27: 925-933

  • DOI: 10.1038/s41594-020-0479-4
  • Primary Citation of Related Structures:  
    6X2A, 6X2C, 6X2B, 6X29

  • PubMed Abstract: 
  • The coronavirus (CoV) spike (S) protein, involved in viral-host cell fusion, is the primary immunogenic target for virus neutralization and the current focus of many vaccine design efforts. The highly flexible S-protein, with its mobile domains, pres ...

    The coronavirus (CoV) spike (S) protein, involved in viral-host cell fusion, is the primary immunogenic target for virus neutralization and the current focus of many vaccine design efforts. The highly flexible S-protein, with its mobile domains, presents a moving target to the immune system. Here, to better understand S-protein mobility, we implemented a structure-based vector analysis of available β-CoV S-protein structures. Despite an overall similarity in domain organization, we found that S-proteins from different β-CoVs display distinct configurations. Based on this analysis, we developed two soluble ectodomain constructs for the SARS-CoV-2 S-protein, in which the highly immunogenic and mobile receptor binding domain (RBD) is either locked in the all-RBDs 'down' position or adopts 'up' state conformations more readily than the wild-type S-protein. These results demonstrate that the conformation of the S-protein can be controlled via rational design and can provide a framework for the development of engineered CoV S-proteins for vaccine applications.


    Related Citations: 
    • Controlling the SARS-CoV-2 Spike Glycoprotein Conformation.
      Henderson, R., Edwards, R.J., Mansouri, K., Janowska, K., Stalls, V., Gobeil, S., Kopp, M., Hsu, A., Borgnia, M., Parks, R., Haynes, B.F., Acharya, P.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Duke University, Department of Surgery, Durham, NC, USA. priyamvada.acharya@duke.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinABC1273Severe acute respiratory syndrome coronavirus 2Mutation(s): 4 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM129539
Other privateUnited StatesSF349247
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI100645
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI44371
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIC ES103326

Revision History 

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 1.2: 2020-07-29
    Changes: Data collection, Structure summary
  • Version 1.3: 2020-09-30
    Changes: Database references
  • Version 1.4: 2020-10-21
    Changes: Database references