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 1.3 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: https://doi.org/10.1038/s41586-021-03807-6
  • Primary Citation of Related Structures:  
    7M7W, 7R6W, 7R6X, 7R7N

  • PubMed Abstract: 

    An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape 1-3 , have activity against diverse 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 the development of therapeutic antibodies 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 trade-off 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 cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies that target the angiotensin-converting enzyme 2 (ACE2) receptor-binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we also characterize a 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 that target the RBD, and identify epitopes and features to prioritize for therapeutic development against the current and potential future pandemics.


  • Organizational Affiliation

    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light Chain of Fab domain of monoclonal antibody S309A [auth B]214Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy Chain of Fab domain of monoclonal antibody S309B [auth A]230Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light Chain of Fab domain of monoclonal antibody S2X35C [auth L]219Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy Chain of Fab domain of monoclonal antibody S2X35D [auth H]231Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence 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
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / 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
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
POL
Query on POL

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

Download Ideal Coordinates CCD File 
CA [auth H],
JA [auth R],
O [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description