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- EMDB-36789: Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-36789
TitleNeutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
Map data
Sample
  • Complex: Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
    • Protein or peptide: ZCP3B4 heavy chain
    • Protein or peptide: ZCP3B4 light chain
    • Protein or peptide: Spike protein S1
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsTang B / Dang S
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: EBioMedicine / Year: 2024
Title: Ultrapotent class I neutralizing antibodies post Omicron breakthrough infection overcome broad SARS-CoV-2 escape variants.
Authors: Mengxiao Luo / Runhong Zhou / Bingjie Tang / Hang Liu / Bohao Chen / Na Liu / Yufei Mo / Pengfei Zhang / Ye Lim Lee / Jonathan Daniel Ip / Allen Wing-Ho Chu / Wan-Mui Chan / Hiu-On Man / ...Authors: Mengxiao Luo / Runhong Zhou / Bingjie Tang / Hang Liu / Bohao Chen / Na Liu / Yufei Mo / Pengfei Zhang / Ye Lim Lee / Jonathan Daniel Ip / Allen Wing-Ho Chu / Wan-Mui Chan / Hiu-On Man / Yuting Chen / Kelvin Kai-Wang To / Kwok-Yung Yuen / Shangyu Dang / Zhiwei Chen /
Abstract: BACKGROUND: The spread of emerging SARS-CoV-2 immune escape sublineages, especially JN.1 and KP.2, has resulted in new waves of COVID-19 globally. The evolving memory B cell responses elicited by the ...BACKGROUND: The spread of emerging SARS-CoV-2 immune escape sublineages, especially JN.1 and KP.2, has resulted in new waves of COVID-19 globally. The evolving memory B cell responses elicited by the parental Omicron variants to subvariants with substantial antigenic drift remain incompletely investigated.
METHODS: Using the single B cell antibody cloning technology, we isolated single memory B cells, delineated the B cell receptor repertoire and conducted the pseudovirus-based assay for recovered ...METHODS: Using the single B cell antibody cloning technology, we isolated single memory B cells, delineated the B cell receptor repertoire and conducted the pseudovirus-based assay for recovered neutralizing antibodies (NAb) screening. We analyzed the cryo-EM structures of top broadly NAbs (bnAbs) and evaluated their in vivo efficacy (golden Syrian hamster model).
FINDINGS: By investigating the evolution of human B cell immunity, we discovered a new panel of bnAbs arising from vaccinees after Omicron BA.2/BA.5 breakthrough infections. Two lead bnAbs ...FINDINGS: By investigating the evolution of human B cell immunity, we discovered a new panel of bnAbs arising from vaccinees after Omicron BA.2/BA.5 breakthrough infections. Two lead bnAbs neutralized major Omicron subvariants including JN.1 and KP.2 with IC values less than 10 ng/mL, representing ultrapotent receptor binding domain (RBD)-specific class I bnAbs. They belonged to the IGHV3-53/3-66 clonotypes instead of evolving from the pre-existing vaccine-induced IGHV1-58/IGKV3-20 bnAb ZCB11. Despite sequence diversity, they targeted previously unrecognized, highly conserved conformational epitopes in the receptor binding motif (RBM) for ultrapotent ACE2 blockade. The lead bnAb ZCP3B4 not only protected the lungs of hamsters intranasally challenged with BA.5.2, BQ.1.1 and XBB.1.5 but also prevented their contact transmission.
INTERPRETATION: Our findings demonstrated that class I bnAbs have evolved an ultrapotent mode of action protecting against highly transmissible and broad Omicron escape variants, and their epitopes ...INTERPRETATION: Our findings demonstrated that class I bnAbs have evolved an ultrapotent mode of action protecting against highly transmissible and broad Omicron escape variants, and their epitopes are potential targets for novel bnAbs and vaccine development.
FUNDING: A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.
History
DepositionJul 10, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36789.png

Downloads & links

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Map

FileDownload / File: emd_36789.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.12072652 - 0.5031104
Average (Standard dev.)0.0024929766 (±0.020541525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_36789_additional_1.map
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Half map: #1

Fileemd_36789_half_map_1.map
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Half map: #2

Fileemd_36789_half_map_2.map
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Sample components

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Entire : Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD

EntireName: Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
Components
  • Complex: Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
    • Protein or peptide: ZCP3B4 heavy chain
    • Protein or peptide: ZCP3B4 light chain
    • Protein or peptide: Spike protein S1

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Supramolecule #1: Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD

SupramoleculeName: Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: ZCP3B4 heavy chain

MacromoleculeName: ZCP3B4 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.947513 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCAASEIIVS SNYMRWVRQA PGKGLEWVSD IYPGGTTYYA DSVKGRFSIS RDNSKNTMYL QMSDLRAED TAVYYCARPI MGGRHGMDVW GQGTTVTVSS

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Macromolecule #2: ZCP3B4 light chain

MacromoleculeName: ZCP3B4 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.62799 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPAS LSASVGDRVT ISCQASQDIN KYLNWYQHKP GRAPKLLIFD ASTLETGVPS RFSGSGSGTH FTLTISSLQP EDIATYYCL QHDHVPLTFG GGTKVEIK

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Macromolecule #3: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.772561 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLCPFDEVFN ATKFPSVYAW ERKKISNCVA DYSVLYNFTP FSAFKCYGVS ATKLNDLCFS NVYADSFVVK GNDVSQIAPG QTGNIADYN YKLPDDFMGC VLAWNTRKID ATSTGNYNYR YRLFRKSNLK PFERDISTEI YQAGNKPCNG VAGVNCYFPL Q SYSFRPTY ...String:
NLCPFDEVFN ATKFPSVYAW ERKKISNCVA DYSVLYNFTP FSAFKCYGVS ATKLNDLCFS NVYADSFVVK GNDVSQIAPG QTGNIADYN YKLPDDFMGC VLAWNTRKID ATSTGNYNYR YRLFRKSNLK PFERDISTEI YQAGNKPCNG VAGVNCYFPL Q SYSFRPTY GVGHQPYRVV VLSFELLHAP ATVCG

UniProtKB: Spike glycoprotein

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215557
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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