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- EMDB-48206: SARS-CoV-2 Wuhan Spike ectodomain in complex with NHP polyclonal ... -

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Basic information

Entry
Database: EMDB / ID: EMD-48206
TitleSARS-CoV-2 Wuhan Spike ectodomain in complex with NHP polyclonal antibody NVX-NHPSA1 (NVX-CoV2373/rS-Beta immunized)
Map dataSARS-CoV-2 Wuhan Spike ectodomain in complex with NHP polyclonal antibody NVX-NHPSA1 (NVX-CoV2373/rS-Beta immunized)
Sample
  • Complex: SARS-CoV-2 Wuhan spike ectodomain in complex with NHP polyclonal antibody NVX-NHPSA1
KeywordsSARS-CoV-2 / spike / NTD / NHP polyclonal antibody / EMPEM / Novavax vaccine / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWard AB / Bangaru S / Jackson AM
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: bioRxiv / Year: 2024
Title: Structural serology of polyclonal antibody responses to mRNA-1273 and NVX-CoV2373 COVID-19 vaccines.
Authors: Sandhya Bangaru / Abigail M Jackson / Jeffrey Copps / Monica L Fernández-Quintero / Jonathan L Torres / Sara T Richey / Bartek Nogal / Leigh M Sewall / Alba Torrents de la Peña / Asma ...Authors: Sandhya Bangaru / Abigail M Jackson / Jeffrey Copps / Monica L Fernández-Quintero / Jonathan L Torres / Sara T Richey / Bartek Nogal / Leigh M Sewall / Alba Torrents de la Peña / Asma Rehman / Mimi Guebre-Xabier / Bethany Girard / Rituparna Das / Kizzmekia S Corbett-Helaire / Robert A Seder / Barney S Graham / Darin K Edwards / Nita Patel / Gale Smith / Andrew B Ward /
Abstract: Current COVID-19 vaccines are largely limited in their ability to induce broad, durable immunity against emerging viral variants. Design and development of improved vaccines utilizing existing ...Current COVID-19 vaccines are largely limited in their ability to induce broad, durable immunity against emerging viral variants. Design and development of improved vaccines utilizing existing platforms requires an in-depth understanding of the antigenic and immunogenic properties of available vaccines. Here we examined the antigenicity of two of the original COVID-19 vaccines, mRNA-1273 and NVX-CoV2373, by electron microscopy-based polyclonal epitope mapping (EMPEM) of serum from immunized non-human primates (NHPs) and clinical trial donors. Both vaccines induce diverse polyclonal antibody (pAb) responses to the N-terminal domain (NTD) in addition to the receptor-binding domain (RBD) of the Spike protein, with the NTD supersite being an immunodominant epitope. High-resolution cryo-EMPEM studies revealed extensive pAb responses to and around the supersite with unique angles of approach and engagement. NTD supersite pAbs were also the most susceptible to variant mutations compared to other specificities, indicating that ongoing Spike ectodomain-based vaccine design strategies should consider immuno-masking this site to prevent induction of these strain-specific responses.
History
DepositionDec 6, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48206.png

Downloads & links

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Map

FileDownload / File: emd_48206.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 Wuhan Spike ectodomain in complex with NHP polyclonal antibody NVX-NHPSA1 (NVX-CoV2373/rS-Beta immunized)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 380 pix.
= 397.1 Å		1.05 Å/pix.
x 380 pix.
= 397.1 Å		1.05 Å/pix.
x 380 pix.
= 397.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.00975517 - 0.034329377
Average (Standard dev.)0.00003507992 (±0.0013254646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 397.09998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48206_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half Map A

Fileemd_48206_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48206_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 Wuhan spike ectodomain in complex with NHP polyclonal ...

EntireName: SARS-CoV-2 Wuhan spike ectodomain in complex with NHP polyclonal antibody NVX-NHPSA1
Components
  • Complex: SARS-CoV-2 Wuhan spike ectodomain in complex with NHP polyclonal antibody NVX-NHPSA1

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Supramolecule #1: SARS-CoV-2 Wuhan spike ectodomain in complex with NHP polyclonal ...

SupramoleculeName: SARS-CoV-2 Wuhan spike ectodomain in complex with NHP polyclonal antibody NVX-NHPSA1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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

Concentration0.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTris-ClTris chloride
150.0 mMNaClSodium chloride

Details: 1X TBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 7942 / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 481305
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 22488
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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