7S3N | pdb_00007s3n

SARS-CoV-2 S stem helix peptide bound to Fab22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.235 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7S3N

This is version 2.2 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.

Macromolecule Content 

  • Total Structure Weight: 50.02 kDa 
  • Atom Count: 3,752 
  • Modeled Residue Count: 440 
  • Deposited Residue Count: 458 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein19Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab22 Heavy ChainB [auth H]223Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab22 Light ChainC [auth L]216Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.246α = 90
b = 73.08β = 100.5
c = 89.043γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
Cootmodel building
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI127521

Revision History  (Full details and data files)

  • 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 2.0: 2022-08-10
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-13
    Changes: Structure summary