7S3M | pdb_00007s3m

MERS-CoV S stem helix peptide bound to Fab22

• PDB DOI: https://doi.org/10.2210/pdb7S3M/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Middle East respiratory syndrome-related coronavirus, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-09-07 Released: 2021-10-27 
• Deposition Author(s): Goldsmith, J.A., McLellan, J.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.252 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Stabilized coronavirus spike stem elicits a broadly protective antibody.

Hsieh, C.L., Werner, A.P., Leist, S.R., Stevens, L.J., Falconer, E., Goldsmith, J.A., Chou, C.W., Abiona, O.M., West, A., Westendorf, K., Muthuraman, K., Fritch, E.J., Dinnon 3rd, K.H., Schafer, A., Denison, M.R., Chappell, J.D., Baric, R.S., Graham, B.S., Corbett, K.S., McLellan, J.S.

(2021) Cell Rep 37: 109929-109929

• PubMed: 34710354 
• DOI: https://doi.org/10.1016/j.celrep.2021.109929
• Primary Citation Related Structures: 
  7S3M, 7S3N


• PubMed Abstract: 
  

  Current coronavirus (CoV) vaccines primarily target immunodominant epitopes in the S1 subunit, which are poorly conserved and susceptible to escape mutations, thus threatening vaccine efficacy. Here, we use structure-guided protein engineering to remove the S1 subunit from the Middle East respiratory syndrome (MERS)-CoV spike (S) glycoprotein and develop stabilized stem (SS) antigens. Vaccination with MERS SS elicits cross-reactive β-CoV antibody responses and protects mice against lethal MERS-CoV challenge. High-throughput screening of antibody-secreting cells from MERS SS-immunized mice led to the discovery of a panel of cross-reactive monoclonal antibodies. Among them, antibody IgG22 binds with high affinity to both MERS-CoV and severe acute respiratory syndrome (SARS)-CoV-2 S proteins, and a combination of electron microscopy and crystal structures localizes the epitope to a conserved coiled-coil region in the S2 subunit. Passive transfer of IgG22 protects mice against both MERS-CoV and SARS-CoV-2 challenge. Collectively, these results provide a proof of principle for cross-reactive CoV antibodies and inform the development of pan-CoV vaccines and therapeutic antibodies.

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Organizational Affiliation: 
• Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.78 kDa 
• Atom Count: 3,509 
• Modeled Residue Count: 450 
• Deposited Residue Count: 456 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	15	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N5Q8  Go to UniProtKB:  K9N5Q8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab22 Heavy Chain	B [auth H]	223	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab22 Light Chain	C [auth L]	218	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.252 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.158	α = 90
b = 123.158	β = 90
c = 97.183	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-27 
Deposition Author(s): Goldsmith, J.A., McLellan, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI127521

Revision History  

• Version 1.0: 2021-10-27
  Type: Initial release
  
• Version 1.1: 2021-11-10
  Changes: Database references
• Version 1.2: 2021-11-17
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary