8SK5

Crystal structure of the SARS-CoV-2 neutralizing VHH 7A9 bound to the spike receptor binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery and multimerization of cross-reactive single-domain antibodies against SARS-like viruses to enhance potency and address emerging SARS-CoV-2 variants.

Hollingsworth, S.A.Noland, C.L.Vroom, K.Saha, A.Sam, M.Gao, Q.Zhou, H.Grandy, D.U.Singh, S.Wen, Z.Warren, C.Ma, X.S.Malashock, D.Galli, J.Go, G.Eddins, M.Mayhood, T.Sathiyamoorthy, K.Fridman, A.Raoufi, F.Gomez-Llorente, Y.Patridge, A.Tang, Y.Chen, S.J.Bailly, M.Ji, C.Kingsley, L.J.Cheng, A.C.Geierstanger, B.H.Gorman, D.M.Zhang, L.Pande, K.

(2023) Sci Rep 13: 13668-13668

  • DOI: https://doi.org/10.1038/s41598-023-40919-7
  • Primary Citation of Related Structures:  
    8SK5

  • PubMed Abstract: 

    Coronaviruses have been the causative agent of three epidemics and pandemics in the past two decades, including the ongoing COVID-19 pandemic. A broadly-neutralizing coronavirus therapeutic is desirable not only to prevent and treat COVID-19, but also to provide protection for high-risk populations against future emergent coronaviruses. As all coronaviruses use spike proteins on the viral surface to enter the host cells, and these spike proteins share sequence and structural homology, we set out to discover cross-reactive biologic agents targeting the spike protein to block viral entry. Through llama immunization campaigns, we have identified single domain antibodies (VHHs) that are cross-reactive against multiple emergent coronaviruses (SARS-CoV, SARS-CoV-2, and MERS). Importantly, a number of these antibodies show sub-nanomolar potency towards all SARS-like viruses including emergent CoV-2 variants. We identified nine distinct epitopes on the spike protein targeted by these VHHs. Further, by engineering VHHs targeting distinct, conserved epitopes into multi-valent formats, we significantly enhanced their neutralization potencies compared to the corresponding VHH cocktails. We believe this approach is ideally suited to address both emerging SARS-CoV-2 variants during the current pandemic as well as potential future pandemics caused by SARS-like coronaviruses.


  • Organizational Affiliation

    Computational and Structural Chemistry, Merck & Co., Inc., 213 East Grand Ave., South San Francisco, CA, 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1231Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-SARS-CoV-2 receptor binding domain VHH165Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.903α = 90
b = 93.903β = 90
c = 121.386γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary