8U1G | pdb_00008u1g

Prefusion-stabilized SARS-CoV-2 S2 subunit

• PDB DOI: https://doi.org/10.2210/pdb8U1G/pdb

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


• Deposited: 2023-08-31 Released: 2024-01-24 
• Deposition Author(s): Hsieh, C.-L., McLellan, J.S.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.262 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge.

Hsieh, C.L., Leist, S.R., Miller, E.H., Zhou, L., Powers, J.M., Tse, A.L., Wang, A., West, A., Zweigart, M.R., Schisler, J.C., Jangra, R.K., Chandran, K., Baric, R.S., McLellan, J.S.

(2024) Nat Commun 15: 1553-1553

• PubMed: 38378768 
• DOI: https://doi.org/10.1038/s41467-024-45404-x
• Primary Citation Related Structures: 
  8U1G


• PubMed Abstract: 
  

  Ever-evolving SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of therapeutic antibodies and vaccines. Developing a coronavirus vaccine that offers a greater breadth of protection against current and future VOCs would eliminate the need to reformulate COVID-19 vaccines. Here, we rationally engineer the sequence-conserved S2 subunit of the SARS-CoV-2 spike protein and characterize the resulting S2-only antigens. Structural studies demonstrate that the introduction of interprotomer disulfide bonds can lock S2 in prefusion trimers, although the apex samples a continuum of conformations between open and closed states. Immunization with prefusion-stabilized S2 constructs elicits broadly neutralizing responses against several sarbecoviruses and protects female BALB/c mice from mouse-adapted SARS-CoV-2 lethal challenge and partially protects female BALB/c mice from mouse-adapted SARS-CoV lethal challenge. These engineering and immunogenicity results should inform the development of next-generation pan-coronavirus therapeutics and vaccines.

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Organizational Affiliation: 
• Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
Department of Medicine-Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, 71103, USA.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.84 kDa 
• Atom Count: 6,244 
• Modeled Residue Count: 809 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2	A, B	530	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.262 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.99	α = 90
b = 78.99	β = 90
c = 479.53	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Hsieh, C.-L., McLellan, J.S.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	--

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release
  
• Version 1.1: 2024-08-07
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Structure summary