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- EMDB-47588: Negative stain EM map of polyclonal serum from mouse immunized wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-47588
TitleNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P
Map dataNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P.
Sample
  • Complex: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabilized with 2P mutations with polyclonal Fabs from mice immunized with MERS-CoV RBD-I53-50.
KeywordsFab / serum / immune complex / MERS-S2P / VIRAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsChao CW / King NP
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI167966 United States
National Science Foundation (NSF, United States)DGE-2140004 United States
CitationJournal: Cell Rep / Year: 2024
Title: Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV.
Authors: Cara W Chao / Kaitlin R Sprouse / Marcos C Miranda / Nicholas J Catanzaro / Miranda L Hubbard / Amin Addetia / Cameron Stewart / Jack T Brown / Annie Dosey / Adian Valdez / Rashmi ...Authors: Cara W Chao / Kaitlin R Sprouse / Marcos C Miranda / Nicholas J Catanzaro / Miranda L Hubbard / Amin Addetia / Cameron Stewart / Jack T Brown / Annie Dosey / Adian Valdez / Rashmi Ravichandran / Grace G Hendricks / Maggie Ahlrichs / Craig Dobbins / Alexis Hand / Jackson McGowan / Boston Simmons / Catherine Treichel / Isabelle Willoughby / Alexandra C Walls / Andrew T McGuire / Elizabeth M Leaf / Ralph S Baric / Alexandra Schäfer / David Veesler / Neil P King /
Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a betacoronavirus that causes severe respiratory illness in humans. There are no licensed vaccines against MERS-CoV and only a few ...Middle East respiratory syndrome coronavirus (MERS-CoV) is a betacoronavirus that causes severe respiratory illness in humans. There are no licensed vaccines against MERS-CoV and only a few candidates in phase I clinical trials. Here, we develop MERS-CoV vaccines utilizing a computationally designed protein nanoparticle platform that has generated safe and immunogenic vaccines against various enveloped viruses, including a licensed vaccine for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two-component nanoparticles displaying spike (S)-derived antigens induce neutralizing responses and protect mice against challenge with mouse-adapted MERS-CoV. Epitope mapping reveals the dominant responses elicited by immunogens displaying the prefusion-stabilized S-2P trimer, receptor binding domain (RBD), or N-terminal domain (NTD). An RBD nanoparticle elicits antibodies targeting multiple non-overlapping epitopes in the RBD. Our findings demonstrate the potential of two-component nanoparticle vaccine candidates for MERS-CoV and suggest that this platform technology could be broadly applicable to betacoronavirus vaccine development.
History
DepositionOct 31, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47588.png

Downloads & links

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Map

FileDownload / File: emd_47588.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.49 Å/pix.
x 260 pix.
= 647.4 Å		2.49 Å/pix.
x 260 pix.
= 647.4 Å		2.49 Å/pix.
x 260 pix.
= 647.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.49 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.13
Minimum - Maximum-1.7825919 - 4.828818
Average (Standard dev.)-0.017886698 (±0.17028254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 647.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Negative stain EM map of polyclonal serum from...

Fileemd_47588_half_map_1.map
AnnotationNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain EM map of polyclonal serum from...

Fileemd_47588_half_map_2.map
AnnotationNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabili...

EntireName: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabilized with 2P mutations with polyclonal Fabs from mice immunized with MERS-CoV RBD-I53-50.
Components
  • Complex: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabilized with 2P mutations with polyclonal Fabs from mice immunized with MERS-CoV RBD-I53-50.

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Supramolecule #1: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabili...

SupramoleculeName: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabilized with 2P mutations with polyclonal Fabs from mice immunized with MERS-CoV RBD-I53-50.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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: 8
StainingType: NEGATIVE / Material: Uranyl formate

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Electron microscopy

MicroscopeTFS TALOS L120C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab Initio model generation
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2478
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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