7R6X

SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2E12 Fab, S309 Fab, and S304 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: 
    • SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape
      Starr, T.N., Czudnochowski, N., Liu, Z., Zatta, F., Park, Y.J., Pinto, D., Beltramello, M., Hernandez, P., Cameroni, E., Croll, T.I., Nix, J.C., Chodera, J.D., Whelan, S.P.J., Virgin, H.W., Corti, D., Veesler, D., Bloom, J.D., Snell, G.
      () To be published --: --

    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S304 Fab light chainA [auth L]215Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S304 Fab heavy chainB [auth H]223Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1C [auth R]216Severe 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
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UniProt GroupP0DTC2
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S309 Fab light chainD [auth B]214Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S309 Fab heavy chainE [auth A]230Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S2E12 Fab light chainF [auth D]216Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody S2E12 Fab heavy chainG [auth C]226Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth R]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth R],
J [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 245.87α = 90
b = 245.87β = 90
c = 237.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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