7R6W

SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


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.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Light Chain of Fab domain of monoclonal antibody S309A [auth B]214Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy Chain of Fab domain of monoclonal antibody S309B [auth A]230Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Light Chain of Fab domain of monoclonal antibody S2X35C [auth L]219Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy Chain of Fab domain of monoclonal antibody S2X35D [auth H]231Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1E [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
Entity Groups  
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UniProt GroupP0DTC2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth C]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth L],
BA [auth L],
DA [auth H],
EA [auth H],
FA [auth R],
AA [auth L],
BA [auth L],
DA [auth H],
EA [auth H],
FA [auth R],
G [auth B],
GA [auth R],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
KA [auth R],
N [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth L],
W [auth L],
X [auth L],
Y [auth L],
Z [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth B],
M [auth B],
P [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
POL
Query on POL

Download Ideal Coordinates CCD File 
HA [auth R],
IA [auth R]
N-PROPANOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.267α = 90
b = 239.372β = 90
c = 129.806γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




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