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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 

  • DOI: 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 ...

    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

    Swiss Vaccine Research Institute, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland. giuseppe.pantaleo@chuv.ch.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
P2G3 Heavy ChainC [auth B],
A [auth G],
G [auth I]
228Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
P2G3 Light ChainD [auth C],
B [auth H],
H [auth J]
214Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
P5C3 Light ChainE215Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
P5C3 Heavy ChainF221Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein,Envelope glycoproteinK [auth A],
I [auth D],
J [auth K]
1285Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
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Go to UniProtKB:  P0DTC2
Find proteins for M1E1E4 (Human immunodeficiency virus 1)
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Go to UniProtKB:  M1E1E4
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UniProt GroupsP0DTC2M1E1E4
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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-glucopyranose
L, M, N, O, P, Q, R, S, T, U, V, W, Y, Z
L, M, N, O, P, Q, R, S, T, U, V, W, Y, Z
2N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseX 4N-Glycosylation Oligosaccharides Interaction
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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