9ECX | pdb_00009ecx

Crystal structure of the SARS-CoV-2 NTD-targeted neutralizing antibody WRAIR-2008


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.289 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

First-generation N-terminal domain supersite public antibodies retain activity against Omicron-derived lineages and protect mice against Omicron BA.5 challenge.

Dussupt, V.Jensen, J.L.Thomas, P.V.Mendez-Rivera, L.Lal, K.G.Zemil McCrea, M.Swafford, I.Hernandez, J.Sankhala, R.S.Rao, M.Arora, J.Hajduczki, A.Jian, N.Rees, P.A.Showell-De Leon, I.Smith, G.Smith, L.Wasson, D.Schmid, A.Teng, I.T.Zhou, T.Kwong, P.D.Currier, J.R.Reiley, W.W.Paquin-Proulx, D.Polonis, V.R.Collins, N.D.Michael, N.L.Joyce, M.G.Krebs, S.J.

(2025) mBio 16: e0103625-e0103625

  • DOI: https://doi.org/10.1128/mbio.01036-25
  • Primary Citation of Related Structures:  
    9ECX, 9ECY, 9ECZ, 9MI3

  • PubMed Abstract: 

    Monoclonal antibodies to SARS-CoV-2 can offer prophylactic and therapeutic protection against severe disease, with particular utility for immunosuppressed and vulnerable populations. With the constant emergence of new variants, understanding the neutralizing potency of monoclonal antibodies to dynamic spike protein epitopes is crucial. We show that a set of VH1-24-derived N-terminal domain (NTD)-directed antibodies, isolated from a convalescent donor early in the pandemic, displayed remarkable neutralization resilience against many Omicron SARS-CoV-2 variants, including BA.2, BA.5, and BQ.1.1. Neutralization potency to these Omicron variants is associated with slower off-rates to the spike protein. Structural characterization of the most potent NTD antibody, WRAIR-2008, revealed a conserved mode of interaction shared with other antibodies of the same multi-donor class. WRAIR-2008 protected mice from weight loss following BA.5 challenge and reduced infectious viral titers in the lungs. Our study highlights the retention of neutralization activity and protection of first-generation VH1-24-derived NTD-directed antibodies to specific Omicron variants and provides valuable insights into the shifting landscape of SARS-CoV-2 variants that are vulnerable to select monoclonal antibodies. As SARS-CoV-2 circulating variants evolve, it is important to understand the vulnerabilities of these viruses to neutralizing antibodies. Within this manuscript, we describe first-generation antibodies isolated following infection with WA-1 that retain viral neutralization to subsequent Omicron variants by targeting a site of viral vulnerability called the NTD. This work highlights the shifting landscape of SARS-CoV-2 variants and provides mechanistic insights into how antibodies from prior infections may play a role in preventing subsequent SARS-CoV-2 variant infections.


  • Organizational Affiliation
    • Viral Diseases Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WRAIR-2008 Fab heavy chainA [auth H],
C
231Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WRAIR-2008 Fab light chainB [auth L],
D
219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth L],
K [auth C],
L [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth H]
F [auth H]
G [auth H]
I [auth L]
J [auth L]
E [auth H],
F [auth H],
G [auth H],
I [auth L],
J [auth L],
M [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.289 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.04α = 90
b = 60.4β = 99.2
c = 92.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH-18-2-0040

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references
  • Version 1.2: 2025-10-22
    Changes: Database references