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- PDB-7qtk: SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD down - 1-P2G3 Fab (Local) -

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Basic information

Entry
Database: PDB / ID: 7qtk
TitleSARS-CoV-2 S Omicron Spike B.1.1.529 - RBD down - 1-P2G3 Fab (Local)
Components
  • P2G3 Heavy Chain
  • P2G3 Light Chain
  • Surface glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 S Omicron Spike B.1.1.529
Function / homologySurface glycoprotein
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsNi, D. / Lau, K. / Turelli, P. / Fenwick, C. / Perez, L. / Pojer, F. / Stahlberg, H. / Pantaleo, G. / Trono, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Microbiol / Year: 2022
Title: Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys.
Authors: Craig Fenwick / Priscilla Turelli / Dongchun Ni / Laurent Perez / Kelvin Lau / Cécile Herate / Romain Marlin / Erica Lana / Céline Pellaton / Charlène Raclot / Line Esteves-Leuenberger / ...Authors: Craig Fenwick / Priscilla Turelli / Dongchun Ni / Laurent Perez / Kelvin Lau / Cécile Herate / Romain Marlin / Erica Lana / Céline Pellaton / Charlène Raclot / Line Esteves-Leuenberger / Jérémy Campos / Alex Farina / Flurin Fiscalini / Nathalie Dereuddre-Bosquet / Francis Relouzat / Rana Abdelnabi / Caroline S Foo / Johan Neyts / Pieter Leyssen / Yves Lévy / Florence Pojer / Henning Stahlberg / Roger LeGrand / Didier Trono / Giuseppe Pantaleo /
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- ...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.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Surface glycoprotein
B: P2G3 Heavy Chain
C: P2G3 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,8674
Polymers190,4423
Non-polymers4241
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5830 Å2
ΔGint-27 kcal/mol
Surface area31590 Å2

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Components

#1: Protein Surface glycoprotein


Mass: 142558.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A8A4XEV3
#2: Antibody P2G3 Heavy Chain


Mass: 24562.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody P2G3 Light Chain


Mass: 23321.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Spike Omicron trimer with Fabs / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5 / Details: PBS
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
4cryoSPARC3.3.1CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
14cryoSPARC3.3.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21672 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 7QO7

7qo7

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025132
ELECTRON MICROSCOPYf_angle_d0.5686977
ELECTRON MICROSCOPYf_dihedral_angle_d4.609712
ELECTRON MICROSCOPYf_chiral_restr0.045775
ELECTRON MICROSCOPYf_plane_restr0.004896

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