6X2B | pdb_00006x2b

SARS-CoV-2 u1S2q 2-RBD Up Spike Protein Trimer

• PDB DOI: https://doi.org/10.2210/pdb6X2B/pdb
• EM Map EMD-22000: EMDB EMDataResource

• 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 32699321 
• DOI: https://doi.org/10.1038/s41594-020-0479-4
• Primary Citation Related Structures: 
  6X29, 6X2A, 6X2B, 6X2C


• 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, 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.

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Organizational Affiliation: 
• Duke Human Vaccine Institute, Durham, NC, USA. [e-mail].
Duke University, Department of Medicine, Durham, NC, USA. [e-mail].
Duke Human Vaccine Institute, Durham, NC, USA.
Duke University, Department of Medicine, Durham, NC, USA.
Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Durham, NC, USA.
Duke University, Department of Immunology, Durham, NC, USA.
Duke Human Vaccine Institute, Durham, NC, USA. [e-mail].
Duke University, Department of Surgery, Durham, NC, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 422.37 kDa 
• Atom Count: 21,120 
• Modeled Residue Count: 2,861 
• Deposited Residue Count: 3,819 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 4  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Henderson, R., Acharya, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM129539
Other private	United States	SF349247
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI100645
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI44371
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ZIC ES103326

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-06-24
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Coordinate replacement
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-09-30
  Changes: Database references
• Version 2.2: 2020-10-21
  Changes: Database references
• Version 2.3: 2021-02-10
  Changes: Structure summary
• Version 3.0: 2021-08-04
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary