7QTI

SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys.

Fenwick, C.Turelli, P.Ni, D.Perez, L.Lau, K.Herate, C.Marlin, R.Lana, E.Pellaton, C.Raclot, C.Esteves-Leuenberger, L.Campos, J.Farina, A.Fiscalini, F.Dereuddre-Bosquet, N.Relouzat, F.Abdelnabi, R.Foo, C.S.Neyts, J.Leyssen, P.Levy, Y.Pojer, F.Stahlberg, H.LeGrand, R.Trono, D.Pantaleo, G.

(2022) Nat Microbiol 7: 1376-1389

  • DOI: https://doi.org/10.1038/s41564-022-01198-6
  • Primary Citation of Related Structures:  
    7QTI, 7QTJ, 7QTK

  • PubMed Abstract: 

    The SARS-CoV-2 Omicron variant has very high levels of transmission, is resistant to neutralization by authorized therapeutic human monoclonal antibodies (mAb) and is less sensitive to vaccine-mediated immunity. To provide additional therapies against Omicron, we isolated a mAb named P2G3 from a previously infected vaccinated donor and showed that it has picomolar-range neutralizing activity against Omicron BA.1, BA.1.1, BA.2 and all other variants tested. We solved the structure of P2G3 Fab in complex with the Omicron spike using cryo-electron microscopy at 3.04 Å resolution to identify the P2G3 epitope as a Class 3 mAb that is different from mAb-binding spike epitopes reported previously. Using a SARS-CoV-2 Omicron monkey challenge model, we show that P2G3 alone, or in combination with P5C3 (a broadly active Class 1 mAb previously identified), confers complete prophylactic or therapeutic protection. Although we could select for SARS-CoV-2 mutants escaping neutralization by P2G3 or by P5C3 in vitro, they had low infectivity and 'escape' mutations are extremely rare in public sequence databases. We conclude that this combination of mAbs has potential as an anti-Omicron drug.


  • Organizational Affiliation

    Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P2G3 Heavy ChainA [auth G],
C [auth B],
G [auth I]
228Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
P2G3 Light ChainB [auth H],
D [auth C],
H [auth J]
214Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
P5C3 Light Chain215Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
P5C3 Heavy Chain221Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein,Envelope glycoproteinI [auth D],
J [auth K],
K [auth A]
1,285Severe 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
Find proteins for M1E1E4 (Human immunodeficiency virus 1)
Explore M1E1E4 
Go to UniProtKB:  M1E1E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTC2M1E1E4
Glycosylation
Glycosylation Sites: 14Go to GlyGen: P0DTC2-1
Sequence Annotations
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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-glucopyranose
L, M, N, O, P
L, M, N, O, P, Q, R, S, T, U, V, W, Y, Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
X
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 8
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-glucopyranoseAA [auth a],
BA [auth b]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2022-09-07
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Refinement description, Structure summary