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- EMDB-48188: SARS-CoV-2 Wuhan Spike ectodomain in complex with human polyclona... -

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Basic information

Entry
Database: EMDB / ID: EMD-48188
TitleSARS-CoV-2 Wuhan Spike ectodomain in complex with human polyclonal antibody ModWu-RBD1 (mRNA-1273 vaccine)
Map data
Sample
  • Complex: SARS-CoV-2 Wuhan Spike ectodomain in complex with human polyclonal antibody ModWu-RBD1
    • Complex: SARS-CoV-2 Wuhan Spike ectodomain
    • Complex: human polyclonal antibody ModWu-RBD1
KeywordsSARS-CoV-2 / spike / human polyclonal antibody / EMPEM / Moderna vaccine / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48188.png

Downloads & links

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Map

FileDownload / File: emd_48188.map.gz / Format: CCP4 / Size: 325 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.)
0.79 Å/pix.
x 440 pix.
= 346.72 Å		0.79 Å/pix.
x 440 pix.
= 346.72 Å		0.79 Å/pix.
x 440 pix.
= 346.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5222869 - 1.1889187
Average (Standard dev.)-0.00026873106 (±0.03838491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 346.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48188_msk_1.map
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Half map: #1

Fileemd_48188_half_map_1.map
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Half map: #2

Fileemd_48188_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 Wuhan Spike ectodomain in complex with human polyclona...

EntireName: SARS-CoV-2 Wuhan Spike ectodomain in complex with human polyclonal antibody ModWu-RBD1
Components
  • Complex: SARS-CoV-2 Wuhan Spike ectodomain in complex with human polyclonal antibody ModWu-RBD1
    • Complex: SARS-CoV-2 Wuhan Spike ectodomain
    • Complex: human polyclonal antibody ModWu-RBD1

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Supramolecule #1: SARS-CoV-2 Wuhan Spike ectodomain in complex with human polyclona...

SupramoleculeName: SARS-CoV-2 Wuhan Spike ectodomain in complex with human polyclonal antibody ModWu-RBD1
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: SARS-CoV-2 Wuhan Spike ectodomain

SupramoleculeName: SARS-CoV-2 Wuhan Spike ectodomain / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: human polyclonal antibody ModWu-RBD1

SupramoleculeName: human polyclonal antibody ModWu-RBD1 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris chloride
150.0 mMSodium chlorideNaCl

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 K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 14094 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 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: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 29000
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: 1148945
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 18968
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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