7N4L

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2125.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.266 

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

Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations.

Dussupt, V.Sankhala, R.S.Mendez-Rivera, L.Townsley, S.M.Schmidt, F.Wieczorek, L.Lal, K.G.Donofrio, G.C.Tran, U.Jackson, N.D.Zaky, W.I.Zemil, M.Tritsch, S.R.Chen, W.H.Martinez, E.J.Ahmed, A.Choe, M.Chang, W.C.Hajduczki, A.Jian, N.Peterson, C.E.Rees, P.A.Rutkowska, M.Slike, B.M.Selverian, C.N.Swafford, I.Teng, I.T.Thomas, P.V.Zhou, T.Smith, C.J.Currier, J.R.Kwong, P.D.Rolland, M.Davidson, E.Doranz, B.J.Mores, C.N.Hatziioannou, T.Reiley, W.W.Bieniasz, P.D.Paquin-Proulx, D.Gromowski, G.D.Polonis, V.R.Michael, N.L.Modjarrad, K.Joyce, M.G.Krebs, S.J.

(2021) Nat Immunol 22: 1503-1514

  • DOI: https://doi.org/10.1038/s41590-021-01068-z
  • Primary Citation of Related Structures:  
    7N4I, 7N4J, 7N4L, 7N4M

  • PubMed Abstract: 

    Prevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.


  • Organizational Affiliation

    Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1205Severe 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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WRAIR-2125 antibody Fab heavy chainB [auth H]232Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
WRAIR-2125 antibody Fab light chainC [auth L]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.266 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.87α = 90
b = 188.87β = 90
c = 65.17γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data 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: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description