7LRT

Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody A23-58.1 that targets the receptor-binding domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants.

Wang, L.Zhou, T.Zhang, Y.Yang, E.S.Schramm, C.A.Shi, W.Pegu, A.Oloniniyi, O.K.Henry, A.R.Darko, S.Narpala, S.R.Hatcher, C.Martinez, D.R.Tsybovsky, Y.Phung, E.Abiona, O.M.Antia, A.Cale, E.M.Chang, L.A.Choe, M.Corbett, K.S.Davis, R.L.DiPiazza, A.T.Gordon, I.J.Hait, S.H.Hermanus, T.Kgagudi, P.Laboune, F.Leung, K.Liu, T.Mason, R.D.Nazzari, A.F.Novik, L.O'Connell, S.O'Dell, S.Olia, A.S.Schmidt, S.D.Stephens, T.Stringham, C.D.Talana, C.A.Teng, I.T.Wagner, D.A.Widge, A.T.Zhang, B.Roederer, M.Ledgerwood, J.E.Ruckwardt, T.J.Gaudinski, M.R.Moore, P.L.Doria-Rose, N.A.Baric, R.S.Graham, B.S.McDermott, A.B.Douek, D.C.Kwong, P.D.Mascola, J.R.Sullivan, N.J.Misasi, J.

(2021) Science 373

  • DOI: https://doi.org/10.1126/science.abh1766
  • Primary Citation of Related Structures:  
    7LRS, 7LRT, 7MLZ, 7MM0

  • PubMed Abstract: 

    The emergence of highly transmissible SARS-CoV-2 variants of concern (VOCs) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identified four receptor binding domain-targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 23 variants, including the B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, and B.1.617 VOCs. Two antibodies are ultrapotent, with subnanomolar neutralization titers [half-maximal inhibitory concentration (IC 50 ) 0.3 to 11.1 nanograms per milliliter; IC 80 1.5 to 34.5 nanograms per milliliter). We define the structural and functional determinants of binding for all four VOC-targeting antibodies and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting their potential in mitigating resistance development.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
antibody A23-58.1 heavy chainA [auth F],
C [auth H],
E [auth D]
228Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
antibody A23-58.1 light chainB [auth G],
D [auth L],
F [auth E]
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SARS-CoV-2 spike glycoproteinG [auth A],
H [auth B],
I [auth C]
1,195Severe 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: 17Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth I],
K [auth J],
L [auth K],
Z
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
M,
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
M,
N,
O,
P,
Q,
R,
T,
U,
V,
W,
X
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseEA [auth e],
S,
Y
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
EB [auth C]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth C],
EB [auth C],
FA [auth A],
FB [auth C],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth B],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references