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- EMDB-43408: Structure of SARS-CoV spike in complex with CoV1-62 IgG -

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Basic information

Entry
Database: EMDB / ID: EMD-43408
TitleStructure of SARS-CoV spike in complex with CoV1-62 IgG
Map dataSharpened map
Sample
  • Complex: Structure of SARS-CoV spike in complex with CoV1-62 IgG
KeywordsSARS-CoV / Spike / Monoclonal antibody / Complex / RBD / VIRAL PROTEIN
Biological speciesSARS coronavirus Urbani
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBangaru S / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI144462 United States
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: J Clin Invest / Year: 2024
Title: Structural characterization of human monoclonal antibodies targeting uncommon antigenic sites on spike glycoprotein of SARS-CoV.
Authors: Naveenchandra Suryadevara / Nurgun Kose / Sandhya Bangaru / Elad Binshtein / Jennifer Munt / David R Martinez / Alexandra Schäfer / Luke Myers / Trevor D Scobey / Robert H Carnahan / Andrew ...Authors: Naveenchandra Suryadevara / Nurgun Kose / Sandhya Bangaru / Elad Binshtein / Jennifer Munt / David R Martinez / Alexandra Schäfer / Luke Myers / Trevor D Scobey / Robert H Carnahan / Andrew B Ward / Ralph S Baric / James E Crowe /
Abstract: The function of the spike protein N terminal domain (NTD) in coronavirus (CoV) infections is poorly understood. However, some rare antibodies that target the SARS-CoV-2 NTD potently neutralize the ...The function of the spike protein N terminal domain (NTD) in coronavirus (CoV) infections is poorly understood. However, some rare antibodies that target the SARS-CoV-2 NTD potently neutralize the virus. This finding suggests the NTD may contribute, in part, to protective immunity. Pansarbecovirus antibodies are desirable for broad protection, but the NTD region of SARS-CoV and SARS-CoV-2 exhibit a high level of sequence divergence; therefore, cross-reactive NTD-specific antibodies are unexpected, and there is no structure of a SARS-CoV NTD-specific antibody in complex with NTD. Here, we report a monoclonal antibody COV1-65, encoded by the IGHV1-69 gene, that recognizes the NTD of SARS-CoV S protein. A prophylaxis study showed the mAb COV1-65 prevented disease when administered before SARS-CoV challenge of BALB/c mice, an effect that requires intact fragment crystallizable region (Fc) effector functions for optimal protection in vivo. The footprint on the S protein of COV1-65 is near to functional components of the S2 fusion machinery, and the selection of COV1-65 escape mutant viruses identified critical residues Y886H and Q974H, which likely affect the epitope through allosteric effects. Structural features of the mAb COV1-65-SARS-CoV antigen interaction suggest critical antigenic determinants that should be considered in the rational design of sarbecovirus vaccine candidates.
History
DepositionJan 16, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43408.png

Downloads & links

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Map

FileDownload / File: emd_43408.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 580 pix.
= 420.5 Å		0.73 Å/pix.
x 580 pix.
= 420.5 Å		0.73 Å/pix.
x 580 pix.
= 420.5 Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.11094029 - 0.21992601
Average (Standard dev.)-0.00005109665 (±0.006195577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 420.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43408_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_43408_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_43408_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Sample components

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Entire : Structure of SARS-CoV spike in complex with CoV1-62 IgG

EntireName: Structure of SARS-CoV spike in complex with CoV1-62 IgG
Components
  • Complex: Structure of SARS-CoV spike in complex with CoV1-62 IgG

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Supramolecule #1: Structure of SARS-CoV spike in complex with CoV1-62 IgG

SupramoleculeName: Structure of SARS-CoV spike in complex with CoV1-62 IgG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: SARS coronavirus Urbani

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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:
ConcentrationFormulaName
50.0 mMTrisTris
150.0 mMNaClSodium Chloride

Details: 1X TBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Number real images: 5684 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 238843
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 25850
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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