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- EMDB-42875: ACE2 dimer bound to one RBD in membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-42875
TitleACE2 dimer bound to one RBD in membrane
Map data
Sample
  • Complex: ACE2 dimer bound to one RBD in membrane
KeywordsComplex / VIRAL PROTEIN / Cellular Receptor
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 18.0 Å
AuthorsQin Z / Li W / Grunst MW / Mothes W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI163395 United States
CitationJournal: Science / Year: 2024
Title: Structure and inhibition of SARS-CoV-2 spike refolding in membranes.
Authors: Michael W Grunst / Zhuan Qin / Esteban Dodero-Rojas / Shilei Ding / Jérémie Prévost / Yaozong Chen / Yanping Hu / Marzena Pazgier / Shenping Wu / Xuping Xie / Andrés Finzi / José N ...Authors: Michael W Grunst / Zhuan Qin / Esteban Dodero-Rojas / Shilei Ding / Jérémie Prévost / Yaozong Chen / Yanping Hu / Marzena Pazgier / Shenping Wu / Xuping Xie / Andrés Finzi / José N Onuchic / Paul C Whitford / Walther Mothes / Wenwei Li /
Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds the receptor angiotensin converting enzyme 2 (ACE2) and drives virus-host membrane fusion through refolding of its ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds the receptor angiotensin converting enzyme 2 (ACE2) and drives virus-host membrane fusion through refolding of its S2 domain. Whereas the S1 domain contains high sequence variability, the S2 domain is conserved and is a promising pan-betacoronavirus vaccine target. We applied cryo-electron tomography to capture intermediates of S2 refolding and understand inhibition by antibodies to the S2 stem-helix. Subtomogram averaging revealed ACE2 dimers cross-linking spikes before transitioning into S2 intermediates, which were captured at various stages of refolding. Pan-betacoronavirus neutralizing antibodies targeting the S2 stem-helix bound to and inhibited refolding of spike prehairpin intermediates. Combined with molecular dynamics simulations, these structures elucidate the process of SARS-CoV-2 entry and reveal how pan-betacoronavirus S2-targeting antibodies neutralize infectivity by arresting prehairpin intermediates.
History
DepositionNov 18, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42875.png

Downloads & links

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Map

FileDownload / File: emd_42875.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.69 Å/pix.
x 80 pix.
= 215.36 Å		2.69 Å/pix.
x 80 pix.
= 215.36 Å		2.69 Å/pix.
x 80 pix.
= 215.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.692 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.18532199 - 0.2712402
Average (Standard dev.)-0.0000024637059 (±0.051776245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 215.35999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42875_msk_1.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 : ACE2 dimer bound to one RBD in membrane

EntireName: ACE2 dimer bound to one RBD in membrane
Components
  • Complex: ACE2 dimer bound to one RBD in membrane

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Supramolecule #1: ACE2 dimer bound to one RBD in membrane

SupramoleculeName: ACE2 dimer bound to one RBD in membrane / 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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 0.8 µm / Calibrated defocus min: 0.2 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: I3 / Details: No symmetry applied / Number subtomograms used: 2590
ExtractionNumber tomograms: 141 / Number images used: 5916
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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