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- EMDB-28090: Negative stain EM map of SARS-CoV-2 Spike in complex with CoVIC-040 -

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Basic information

Entry
Database: EMDB / ID: EMD-28090
TitleNegative stain EM map of SARS-CoV-2 Spike in complex with CoVIC-040
Map dataNegative stain EM map of SARS-CoV-2 Spike in complex with CoVIC-040
Sample
  • Complex: SARS-CoV-2 D614G HexaPro Spike in complex with CoVIC-040
KeywordsSARS-CoV-2 Spike / Spike / antibody / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 16.3 Å
AuthorsLi H / Callaway H / Yu X / Shek J / Saphire EO
Funding support United States, 3 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-0006133 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790-03S1 United States
GHR Foundation United States
CitationJournal: Cell Rep / Year: 2023
Title: Bivalent intra-spike binding provides durability against emergent Omicron lineages: Results from a global consortium.
Authors: Heather M Callaway / Kathryn M Hastie / Sharon L Schendel / Haoyang Li / Xiaoying Yu / Jeremy Shek / Tierra Buck / Sean Hui / Dan Bedinger / Camille Troup / S Moses Dennison / Kan Li / ...Authors: Heather M Callaway / Kathryn M Hastie / Sharon L Schendel / Haoyang Li / Xiaoying Yu / Jeremy Shek / Tierra Buck / Sean Hui / Dan Bedinger / Camille Troup / S Moses Dennison / Kan Li / Michael D Alpert / Charles C Bailey / Sharon Benzeno / Jody L Bonnevier / Jin-Qiu Chen / Charm Chen / Hyeseon Cho / Peter D Crompton / Vincent Dussupt / Kevin C Entzminger / Yassine Ezzyat / Jonathan K Fleming / Nick Geukens / Amy E Gilbert / Yongjun Guan / Xiaojian Han / Christopher J Harvey / Julia M Hatler / Bryan Howie / Chao Hu / Ailong Huang / Maya Imbrechts / Aishun Jin / Nik Kamachi / Gladys Keitany / Mark Klinger / Jay K Kolls / Shelly J Krebs / Tingting Li / Feiyan Luo / Toshiaki Maruyama / Michael A Meehl / Letzibeth Mendez-Rivera / Andrea Musa / C J Okumura / Benjamin E R Rubin / Aaron K Sato / Meiying Shen / Anirudh Singh / Shuyi Song / Joshua Tan / Jeffrey M Trimarchi / Dhruvkumar P Upadhyay / Yingming Wang / Lei Yu / Tom Z Yuan / Erik Yusko / Bjoern Peters / Georgia Tomaras / Erica Ollmann Saphire /
Abstract: The SARS-CoV-2 Omicron variant of concern (VoC) and its sublineages contain 31-36 mutations in spike and escape neutralization by most therapeutic antibodies. In a pseudovirus neutralization assay, ...The SARS-CoV-2 Omicron variant of concern (VoC) and its sublineages contain 31-36 mutations in spike and escape neutralization by most therapeutic antibodies. In a pseudovirus neutralization assay, 66 of the nearly 400 candidate therapeutics in the Coronavirus Immunotherapeutic Consortium (CoVIC) panel neutralize Omicron and multiple Omicron sublineages. Among natural immunoglobulin Gs (IgGs), especially those in the receptor-binding domain (RBD)-2 epitope community, nearly all Omicron neutralizers recognize spike bivalently, with both antigen-binding fragments (Fabs) simultaneously engaging adjacent RBDs on the same spike. Most IgGs that do not neutralize Omicron bind either entirely monovalently or have some (22%-50%) monovalent occupancy. Cleavage of bivalent-binding IgGs to Fabs abolishes neutralization and binding affinity, with disproportionate loss of activity against Omicron pseudovirus and spike. These results suggest that VoC-resistant antibodies overcome mutagenic substitution via avidity. Hence, vaccine strategies targeting future SARS-CoV-2 variants should consider epitope display with spacing and organization identical to trimeric spike.
History
DepositionSep 9, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28090.png

Downloads & links

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Map

FileDownload / File: emd_28090.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of SARS-CoV-2 Spike in complex with CoVIC-040
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.85 Å/pix.
x 300 pix.
= 555. Å		1.85 Å/pix.
x 300 pix.
= 555. Å		1.85 Å/pix.
x 300 pix.
= 555. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.294
Minimum - Maximum-1.5538586 - 4.0048375
Average (Standard dev.)-0.022114111 (±0.14738941)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 555.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Halfmap A

Fileemd_28090_half_map_1.map
AnnotationHalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap B

Fileemd_28090_half_map_2.map
AnnotationHalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 D614G HexaPro Spike in complex with CoVIC-040

EntireName: SARS-CoV-2 D614G HexaPro Spike in complex with CoVIC-040
Components
  • Complex: SARS-CoV-2 D614G HexaPro Spike in complex with CoVIC-040

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Supramolecule #1: SARS-CoV-2 D614G HexaPro Spike in complex with CoVIC-040

SupramoleculeName: SARS-CoV-2 D614G HexaPro Spike in complex with CoVIC-040
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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

Concentration0.1 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20897
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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