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- EMDB-14143: SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD down - 1-P2G3 Fab (Local) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-14143
TitleSARS-CoV-2 S Omicron Spike B.1.1.529 - RBD down - 1-P2G3 Fab (Local)
Map data
Sample
  • Complex: Spike Omicron trimer with Fabs
    • Protein or peptide: Surface glycoprotein
    • Protein or peptide: P2G3 Heavy Chain
    • Protein or peptide: P2G3 Light Chain
Function / homologySurface glycoprotein
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle 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, 1 items
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, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateSep 7, 2022-
Current statusSep 7, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14143.png

Downloads & links

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Map

FileDownload / File: emd_14143.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 300 pix.
= 414.99 Å		1.38 Å/pix.
x 300 pix.
= 414.99 Å		1.38 Å/pix.
x 300 pix.
= 414.99 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.256
Minimum - Maximum-1.7222005 - 1.9187574
Average (Standard dev.)-0.00022585073 (±0.028901536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 414.99 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Spike Omicron trimer with Fabs

EntireName: Spike Omicron trimer with Fabs
Components
  • Complex: Spike Omicron trimer with Fabs
    • Protein or peptide: Surface glycoprotein
    • Protein or peptide: P2G3 Heavy Chain
    • Protein or peptide: P2G3 Light Chain

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Supramolecule #1: Spike Omicron trimer with Fabs

SupramoleculeName: Spike Omicron trimer with Fabs / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)

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Macromolecule #1: Surface glycoprotein

MacromoleculeName: Surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 142.558094 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DHKNNKSWME SEFRVYSSAN N CTFEYVSQ ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DHKNNKSWME SEFRVYSSAN N CTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPIIVR EPEDLPQGFS ALEPLVDLPI GINITRFQTL LA LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NLAPFFTFKC YGVSPTKLND LCFTNVYADS FVIR GDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVSGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGV AGFN CYFPLRSYSF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLK GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHGSAS SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFS QILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFKGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTA SALGKLQDVV NHNAQALNTL V KQLSSKFG AISSVLNDIF SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSH PQFE K

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Macromolecule #2: P2G3 Heavy Chain

MacromoleculeName: P2G3 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.562475 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LVQPGRSLRL SCAASGFRFD DYALHWVRQA PEKGLEWVSG ISWNSNNIGY AESVKGRFTI SRDTAKKSLY LQMNDLRAE DTALYYCVKD RHYDSSGYFV NGFDIWGQGT LVTVSAASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EVQLVESGGG LVQPGRSLRL SCAASGFRFD DYALHWVRQA PEKGLEWVSG ISWNSNNIGY AESVKGRFTI SRDTAKKSLY LQMNDLRAE DTALYYCVKD RHYDSSGYFV NGFDIWGQGT LVTVSAASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC

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Macromolecule #3: P2G3 Light Chain

MacromoleculeName: P2G3 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.321771 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQLTQSPSF LSASVGDRVT VTCRASQGIS SYVAWYQQKA GKAPTLLIYT ASTLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QLHSYPVTFG QGTRLDIERT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQLTQSPSF LSASVGDRVT VTCRASQGIS SYVAWYQQKA GKAPTLLIYT ASTLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QLHSYPVTFG QGTRLDIERT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.5 / Details: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1)
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 21672
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7qo7

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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