7LS9

Cryo-EM structure of neutralizing antibody 1-57 in complex with prefusion SARS-CoV-2 spike glycoprotein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for accommodation of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing antibodies.

Cerutti, G.Rapp, M.Guo, Y.Bahna, F.Bimela, J.Reddem, E.R.Yu, J.Wang, P.Liu, L.Huang, Y.Ho, D.D.Kwong, P.D.Sheng, Z.Shapiro, L.

(2021) Structure 29: 655-663.e4

  • DOI: https://doi.org/10.1016/j.str.2021.05.014
  • Primary Citation of Related Structures:  
    7LS9, 7LSS

  • PubMed Abstract: 

    Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively, show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical concern. However, the neutralization potency of two antibodies, 1-57 and 2-7, which target the receptor-binding domain (RBD) of the spike, was unaffected by these emerging strains. Here, we report cryo-EM structures of 1-57 and 2-7 in complex with spike, revealing each of these antibodies to utilize a distinct mechanism to bypass or accommodate RBD mutations. Notably, each antibody represented an immune response with recognition distinct from those of frequent antibody classes. Moreover, many epitope residues recognized by 1-57 and 2-7 were outside hotspots of evolutionary pressure for ACE2 binding and neutralizing antibody escape. We suggest the therapeutic use of antibodies, such as 1-57 and 2-7, which target less prevalent epitopes, could ameliorate issues of monoclonal antibody escape.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA.


Macromolecules
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Entity ID: 1
Molecule Chains  Sequence Length Organism Details Image
Spike glycoprotein A,
D [auth B],
G [auth C]
1,288 Severe acute respiratory syndrome coronavirus 2 Mutation(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 Group P0DTC2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
Molecule Chains  Sequence Length Organism Details Image
1-57 Fab heavy chain B [auth H],
E [auth D],
H [auth E]
244 Homo sapiens Mutation(s): 0 
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Entity ID: 3
Molecule Chains  Sequence Length Organism Details Image
1-57 Fab light chain C [auth L],
F,
I [auth G]
215 Homo sapiens Mutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
Molecule Chains  Length 2D Diagram  Glycosylation 3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose J [auth I],
Q [auth K],
X [auth P]
3 N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
ID Chains  Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
EA [auth A]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth C],
EA [auth A],
EB [auth C],
FA [auth A],
FB [auth C],
GA [auth A],
GB [auth C],
HA [auth A],
HB [auth C],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
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: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
Task Software Package Version
RECONSTRUCTION cryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding Organization Location Grant Number
Jack Ma Foundation China --

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references
  • Version 1.3: 2021-09-29
    Changes: Database references