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- EMDB-26432: Structure of the SARS-CoV-2 S 6P trimer in complex with the neutr... -

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Basic information

Entry
Database: EMDB / ID: EMD-26432
TitleStructure of the SARS-CoV-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1791
Map dataSharpened map
Sample
  • Complex: SARS-CoV-2 S 6P + C1791 Fab fragments
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBarnes CO
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)GT15335 United States
CitationJournal: Immunity / Year: 2022
Title: Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins.
Authors: Zijun Wang / Frauke Muecksch / Alice Cho / Christian Gaebler / Hans-Heinrich Hoffmann / Victor Ramos / Shuai Zong / Melissa Cipolla / Briana Johnson / Fabian Schmidt / Justin DaSilva / Eva ...Authors: Zijun Wang / Frauke Muecksch / Alice Cho / Christian Gaebler / Hans-Heinrich Hoffmann / Victor Ramos / Shuai Zong / Melissa Cipolla / Briana Johnson / Fabian Schmidt / Justin DaSilva / Eva Bednarski / Tarek Ben Tanfous / Raphael Raspe / Kaihui Yao / Yu E Lee / Teresia Chen / Martina Turroja / Katrina G Milard / Juan Dizon / Anna Kaczynska / Anna Gazumyan / Thiago Y Oliveira / Charles M Rice / Marina Caskey / Paul D Bieniasz / Theodora Hatziioannou / Christopher O Barnes / Michel C Nussenzweig /
Abstract: SARS-CoV-2 infection or vaccination produces neutralizing antibody responses that contribute to better clinical outcomes. The receptor-binding domain (RBD) and the N-terminal domain (NTD) of the ...SARS-CoV-2 infection or vaccination produces neutralizing antibody responses that contribute to better clinical outcomes. The receptor-binding domain (RBD) and the N-terminal domain (NTD) of the spike trimer (S) constitute the two major neutralizing targets for antibodies. Here, we use NTD-specific probes to capture anti-NTD memory B cells in a longitudinal cohort of infected individuals, some of whom were vaccinated. We found 6 complementation groups of neutralizing antibodies. 58% targeted epitopes outside the NTD supersite, 58% neutralized either Gamma or Omicron, and 14% were broad neutralizers that also neutralized Omicron. Structural characterization revealed that broadly active antibodies targeted three epitopes outside the NTD supersite including a class that recognized both the NTD and SD2 domain. Rapid recruitment of memory B cells producing these antibodies into the plasma cell compartment upon re-infection likely contributes to the relatively benign course of subsequent infections with SARS-CoV-2 variants, including Omicron.
History
DepositionMar 13, 2022-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26432.png

Downloads & links

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Map

FileDownload / File: emd_26432.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 216 pix.
= 368.064 Å		1.7 Å/pix.
x 216 pix.
= 368.064 Å		1.7 Å/pix.
x 216 pix.
= 368.064 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.704 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.0778604 - 2.9722803
Average (Standard dev.)-0.004177968 (±0.10670568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 368.064 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_26432_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26432_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26432_half_map_2.map
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 S 6P + C1791 Fab fragments

EntireName: SARS-CoV-2 S 6P + C1791 Fab fragments
Components
  • Complex: SARS-CoV-2 S 6P + C1791 Fab fragments

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Supramolecule #1: SARS-CoV-2 S 6P + C1791 Fab fragments

SupramoleculeName: SARS-CoV-2 S 6P + C1791 Fab fragments / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Details: Complex between soluble SARS-CoV-2 S 6P bound to C1791 Fab fragments
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293
Molecular weightExperimental: 700 KDa

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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

Concentration3.0 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5206 / Average exposure time: 3.0 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: 2.5 µm / Nominal defocus min: 1.0 µm
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: 779800
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2)
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 257978
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2) / Details: ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationNumber classes: 6 / Avg.num./class: 100000 / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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