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 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 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence AnnotationsExpand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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 AnnotationsExpand
  • 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 AnnotationsExpand
  • 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

View Full Validation Report



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
  • Version 1.1: 2024-11-13
    Changes: Structure summary