7M7W

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.

Starr, T.N., Czudnochowski, N., Liu, Z., Zatta, F., Park, Y.J., Addetia, A., Pinto, D., Beltramello, M., Hernandez, P., Greaney, A.J., Marzi, R., Glass, W.G., Zhang, I., Dingens, A.S., Bowen, J.E., Tortorici, M.A., Walls, A.C., Wojcechowskyj, J.A., De Marco, A., Rosen, L.E., Zhou, J., Montiel-Ruiz, M., Kaiser, H., Dillen, J.R., Tucker, H., Bassi, J., Silacci-Fregni, C., Housley, M.P., di Iulio, J., Lombardo, G., Agostini, M., Sprugasci, N., Culap, K., Jaconi, S., Meury, M., Dellota Jr., E., Abdelnabi, R., Foo, S.C., Cameroni, E., Stumpf, S., Croll, T.I., Nix, J.C., Havenar-Daughton, C., Piccoli, L., Benigni, F., Neyts, J., Telenti, A., Lempp, F.A., Pizzuto, M.S., Chodera, J.D., Hebner, C.M., Virgin, H.W., Whelan, S.P.J., Veesler, D., Corti, D., Bloom, J.D., Snell, G.

(2021) Nature 597: 97-102

  • DOI: 10.1038/s41586-021-03807-6
  • Primary Citation of Related Structures:  
    7M7W, 7R6W, 7R6X, 7R7N

  • PubMed Abstract: 

    • An ideal anti-SARS-CoV-2 antibody would resist viral escape 1-3 , have activity against diverse SARS-related coronaviruses (sarbecoviruses) 4-7 , and be highly protective through viral neutralization 8-11 and effector functions 12,13 ...

    An ideal anti-SARS-CoV-2 antibody would resist viral escape 1-3 , have activity against diverse SARS-related coronaviruses (sarbecoviruses) 4-7 , and be highly protective through viral neutralization 8-11 and effector functions 12,13 . Understanding how these properties relate to each other and vary across epitopes would aid development of antibody therapeutics and guide vaccine design. Here, we comprehensively characterize escape, breadth, and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD). Despite a tradeoff between in vitro neutralization potency and breadth of sarbecovirus binding, we identify neutralizing antibodies with exceptional sarbecovirus breadth and a corresponding resistance to SARS-CoV-2 escape. One of these antibodies, S2H97, binds with high affinity across all sarbecovirus clades to a previously undescribed cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies targeting the ACE2 receptor binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we characterize one potent RBM antibody (S2E12 8 ) with breadth across sarbecoviruses related to SARS-CoV-2 and a high barrier to viral escape. These data highlight principles underlying variation in escape, breadth, and potency among antibodies targeting the RBD, and identify epitopes and features to prioritize for therapeutic development against the current and potential future pandemics.

    Related Citations: 
    • Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape.
      Starr, T.N., Czudnochowski, N., Zatta, F., Park, Y.J., Liu, Z., Addetia, A., Pinto, D., Beltramello, M., Hernandez, P., Greaney, A.J., Marzi, R., Glass, W.G., Zhang, I., Dingens, A.S., Bowen, J.E., Wojcechowskyj, J.A., De Marco, A., Rosen, L.E., Zhou, J., Montiel-Ruiz, M., Kaiser, H., Tucker, H., Housley, M.P., di Iulio, J., Lombardo, G., Agostini, M., Sprugasci, N., Culap, K., Jaconi, S., Meury, M., Dellota, E., Cameroni, E., Croll, T.I., Nix, J.C., Havenar-Daughton, C., Telenti, A., Lempp, F.A., Pizzuto, M.S., Chodera, J.D., Hebner, C.M., Whelan, S.P.J., Virgin, H.W., Veesler, D., Corti, D., Bloom, J.D., Snell, G.
      (2021) Biorxiv --: --
    Organizational Affiliation: 

    Vir Biotechnology, San Francisco, CA, 94158, USA. gsnell@vir.bio.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S2X259 Fab light chainA [auth B],
E [auth L]		219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S2X259 Fab heavy chainB [auth A],
F [auth H]		229Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S2H97 Fab light chainC [auth D],
G [auth F]		218Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S2H97 Fab heavy chainD [auth C],
H [auth E]		223Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1J [auth R],
I [auth S]		216Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
K [auth S],
L [auth R]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.185α = 90
b = 66.402β = 94.34
c = 237.659γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references
  • Version 1.2: 2021-07-28
    Changes: Database references
  • Version 1.3: 2021-09-15
    Changes: Database references