8FI9

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 

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Ligand Structure Quality Assessment 


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Literature

Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques.

Sankhala, R.S.Lal, K.G.Jensen, J.L.Dussupt, V.Mendez-Rivera, L.Bai, H.Wieczorek, L.Mayer, S.V.Zemil, M.Wagner, D.A.Townsley, S.M.Hajduczki, A.Chang, W.C.Chen, W.H.Donofrio, G.C.Jian, N.King, H.A.D.Lorang, C.G.Martinez, E.J.Rees, P.A.Peterson, C.E.Schmidt, F.Hart, T.J.Duso, D.K.Kummer, L.W.Casey, S.P.Williams, J.K.Kannan, S.Slike, B.M.Smith, L.Swafford, I.Thomas, P.V.Tran, U.Currier, J.R.Bolton, D.L.Davidson, E.Doranz, B.J.Hatziioannou, T.Bieniasz, P.D.Paquin-Proulx, D.Reiley, W.W.Rolland, M.Sullivan, N.J.Vasan, S.Collins, N.D.Modjarrad, K.Gromowski, G.D.Polonis, V.R.Michael, N.L.Krebs, S.J.Joyce, M.G.

(2024) Nat Commun 15: 200-200

  • DOI: https://doi.org/10.1038/s41467-023-44265-0
  • Primary Citation of Related Structures:  
    8FHY, 8FI9

  • PubMed Abstract: 

    The repeat emergence of SARS-CoV-2 variants of concern (VoC) with decreased susceptibility to vaccine-elicited antibodies highlights the need to develop next-generation vaccine candidates that confer broad protection. Here we describe the antibody response induced by the SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine candidate adjuvanted with the Army Liposomal Formulation including QS21 (ALFQ) in non-human primates. By isolating and characterizing several monoclonal antibodies directed against the Spike Receptor Binding Domain (RBD), N-Terminal Domain (NTD), or the S2 Domain, we define the molecular recognition of vaccine-elicited cross-reactive monoclonal antibodies (mAbs) elicited by SpFN. We identify six neutralizing antibodies with broad sarbecovirus cross-reactivity that recapitulate serum polyclonal antibody responses. In particular, RBD mAb WRAIR-5001 binds to the conserved cryptic region with high affinity to sarbecovirus clades 1 and 2, including Omicron variants, while mAb WRAIR-5021 offers complete protection from B.1.617.2 (Delta) in a murine challenge study. Our data further highlight the ability of SpFN vaccination to stimulate cross-reactive B cells targeting conserved regions of the Spike with activity against SARS CoV-1 and SARS-CoV-2 variants.


  • 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 S1A,
B [auth C],
H [auth K],
K [auth O]
205Severe 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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WRAIR-5001 Fab Light chainC [auth F],
F [auth I],
I [auth L],
J [auth N]
215Macaca mulattaMutation(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-5001 Fab Heavy chainD [auth G],
E [auth H],
G [auth J],
L [auth Q]
223Macaca mulattaMutation(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
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A],
N [auth C],
R [auth K],
V [auth O]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
O [auth H]
P [auth H]
Q [auth J]
S [auth N]
T [auth N]
O [auth H],
P [auth H],
Q [auth J],
S [auth N],
T [auth N],
U [auth N],
W [auth O],
X [auth Q],
Y [auth Q],
Z [auth Q]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.508α = 90
b = 115.565β = 111.97
c = 142.167γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2024-01-17
    Type: Initial release