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- EMDB-70031: Rhesus Macaque L603 wk12 polyFab + SARS-CoV-2 Spike -

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Basic information

Entry
Database: EMDB / ID: EMD-70031
TitleRhesus Macaque L603 wk12 polyFab + SARS-CoV-2 Spike
Map datamain map
Sample
  • Complex: Rhesus Macaque L603 wk12 polyFab + SARS-CoV-2 Spike
KeywordsCoronavirus / Fab / spike / polyclonal / negative stain EM / VIRAL PROTEIN
Biological speciesMacaca (macaques)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsLin RN / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Cell Rep / Year: 2026
Title: Heterologous betacoronavirus spike immunization in non-human primates elicits antibodies that neutralize both sarbeco- and merbecoviruses.
Authors: Katharina Dueker / Tazio Capozzola / Ziqi Feng / Ryan N Lin / Jonathan Hurtado / Sandhya Bangaru / Meng Yuan / Nathan Beutler / Elijah Garcia / Wan-Ting He / Sean Callaghan / Gabriel ...Authors: Katharina Dueker / Tazio Capozzola / Ziqi Feng / Ryan N Lin / Jonathan Hurtado / Sandhya Bangaru / Meng Yuan / Nathan Beutler / Elijah Garcia / Wan-Ting He / Sean Callaghan / Gabriel Avillion / Lina Vo / Xuduo Li / Jonathan L Torres / Rami Musharrafieh / Ge Song / Nitesh Mishra / Pragati Sharma / Peter Yong / Fabio Anzanello / Katarzyna Kaczmarek Michaels / Elana Ben-Akiva / Murillo Silva / Mariane Melo / Muzamil Makhdoomi / Ethan Westfall-Gomez / William Rinaldi / Melissa Ferguson / Yana Safonova / Shane Crotty / Darrell J Irvine / Thomas Rogers / Andrew B Ward / Bryan Briney / Ian A Wilson / Dennis R Burton / Raiees Andrabi /
Abstract: In anticipation of future coronavirus (CoV) pandemics, developing vaccines that elicit broadly neutralizing antibodies (bnAbs) against diverse CoVs is critical. Here, we vaccinated rhesus macaques ...In anticipation of future coronavirus (CoV) pandemics, developing vaccines that elicit broadly neutralizing antibodies (bnAbs) against diverse CoVs is critical. Here, we vaccinated rhesus macaques with the SARS-CoV-2 spike (S)-protein, then boosted with heterologous β-CoV S-proteins to focus responses to common conserved S2 bnAb epitopes. Initial SARS-CoV-2 priming elicited receptor-binding domain (RBD)-focused responses, while MERS-CoV boosting redirected responses toward the S2 region, including the stem-helix bnAb site. Although S2-directed serum cross-neutralization was undetectable and most isolated cross-reactive monoclonal antibodies (mAbs) targeted non-neutralizing epitopes, two S2 stem-helix mAbs were identified from memory B cells. These bnAbs neutralized diverse sarbeco- and merbecoviruses, including MERS-CoV, and conferred robust in vivo protection against SARS-CoV-2 challenge. Structural studies reveal that these macaque bnAbs closely mimic human S2 stem bnAbs induced by infection. These findings provide proof-of-principle for vaccination strategies that elicit broadly protective β-coronavirus responses and highlight non-human primates as a translational model for evaluating S2-targeted immunogens.
History
DepositionApr 4, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70031.png

Downloads & links

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Map

FileDownload / File: emd_70031.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 256 pix.
= 483.84 Å		1.89 Å/pix.
x 256 pix.
= 483.84 Å		1.89 Å/pix.
x 256 pix.
= 483.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.02974122 - 0.09020163
Average (Standard dev.)0.000032608183 (±0.003505909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 483.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map 5

Fileemd_70031_additional_1.map
AnnotationAdditional Map 5
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Additional map: Additional Map 4

Fileemd_70031_additional_2.map
AnnotationAdditional Map 4
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Additional map: Additional Map 3

Fileemd_70031_additional_3.map
AnnotationAdditional Map 3
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Additional map: Additional Map 2

Fileemd_70031_additional_4.map
AnnotationAdditional Map 2
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Additional map: Additional Map 1

Fileemd_70031_additional_5.map
AnnotationAdditional Map 1
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Half map: half map A

Fileemd_70031_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_70031_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : Rhesus Macaque L603 wk12 polyFab + SARS-CoV-2 Spike

EntireName: Rhesus Macaque L603 wk12 polyFab + SARS-CoV-2 Spike
Components
  • Complex: Rhesus Macaque L603 wk12 polyFab + SARS-CoV-2 Spike

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Supramolecule #1: Rhesus Macaque L603 wk12 polyFab + SARS-CoV-2 Spike

SupramoleculeName: Rhesus Macaque L603 wk12 polyFab + SARS-CoV-2 Spike / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca (macaques)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vxx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 5930
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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