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- EMDB-73668: Structure of SS-L2-FerritinNP -

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Basic information

Entry
Database: EMDB / ID: EMD-73668
TitleStructure of SS-L2-FerritinNP
Map data
Sample
  • Complex: Structure of SS-L2-FerritinNP
KeywordsProtein Nanoparticle Vaccine / VIRUS LIKE PARTICLE
Biological speciesMammalian expression vector Flag-MCS-pcDNA3.1 (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.25 Å
AuthorsDzuvor CK / Corbett-Helaire KS
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2025
Title: Unconventional linkers facilitate potent stabilized coronavirus stem antibody responses following nanoparticle vaccination.
Authors: Christian K O Dzuvor / Sydney P Moak / Lindsay R McManus / Abigail E Dzordzorme / Lamount R Evanson / Taewoo Kim / Abigail Thomas / Olayimika Adeyemi / Valerie Foley / Aditi Limaye / Ryan P ...Authors: Christian K O Dzuvor / Sydney P Moak / Lindsay R McManus / Abigail E Dzordzorme / Lamount R Evanson / Taewoo Kim / Abigail Thomas / Olayimika Adeyemi / Valerie Foley / Aditi Limaye / Ryan P McNamara / Kizzmekia S Corbett-Helaire /
Abstract: Vaccine technologies that protect against a range of related pathogens within viral families, such as human immunodeficiency virus (HIV), influenza, and coronaviruses (CoVs) represent the future of ...Vaccine technologies that protect against a range of related pathogens within viral families, such as human immunodeficiency virus (HIV), influenza, and coronaviruses (CoVs) represent the future of viral vaccine development. Towards developing broad-spectrum CoV and influenza vaccines, we and others previously designed and evaluated CoV and influenza stem antigens; but these elicited relatively weak and sub-neutralizing antibody (Ab) responses. Multivalent antigen display on nanoparticles (NPs) is an established strategy to enhance and shape immunogenicity. However, one facet of NP vaccines has been largely overlooked: the indispensable linker segment between the antigen and NP core. Here, we introduce -designed rigid (L2) and rarely used long flexible (L6) linkers to optimally display antigens on NPs, target occluded epitopes, and enhance cross-reactive Ab responses, using prefusion-stabilized Middle East respiratory syndrome coronavirus (MERS-CoV) spike (S-2P) and stem (SS) antigens as prototype antigens. Antigenic characterization of L2-NPs confirmed enhanced Ab binding and exposure of cross-reactive epitopes compared with L6-NPs and soluble antigens. Immunization with SS-L2-NPs elicited broader, more potent cross-reactive Ab responses across the seven human-infecting CoVs and pandemic threat WIV1-CoV, whereas SS-L6-NPs induced stronger neutralizing Ab responses against MERS-CoV, SARS-CoV-2, and WIV1-CoV. Ab competition and systems serology analyses revealed that SS-L2-NPs elicit robust Fc-mediated effector functions. By improving CoV-targeting Ab functionality, these linker approaches have the potential to confer broad-spectrum CoV protection and represent a promising strategy against hypervariable influenza and HIV viruses - as well as other broad viral families with pandemic potential.
History
DepositionOct 29, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73668.png

Downloads & links

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Map

FileDownload / File: emd_73668.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0916
Minimum - Maximum-1.8575926 - 1.624731
Average (Standard dev.)-0.0003332782 (±0.033719204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73668_msk_1.map
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AxesZYX

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Half map: Cryo-EM map half B

Fileemd_73668_half_map_1.map
AnnotationCryo-EM map half B
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Histogram

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Half map: Cryo-EM map half A

Fileemd_73668_half_map_2.map
AnnotationCryo-EM map half A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : Structure of SS-L2-FerritinNP

EntireName: Structure of SS-L2-FerritinNP
Components
  • Complex: Structure of SS-L2-FerritinNP

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Supramolecule #1: Structure of SS-L2-FerritinNP

SupramoleculeName: Structure of SS-L2-FerritinNP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)

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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

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.12 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 70359
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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