Tomogram of SARS-CoV-2 spike-bearing virus-like particles (VLPs) interacting with hACE2-bearing extracellular vesicles (tEVs), showing various intermediate states of the SARS-CoV-2 spike protein (Fig. 4B-E and Supp. Movie 3 of manuscript Marcink et al., 2021).
Map data
Tomogram of SARS-CoV-2 spike-bearing virus-like particles (VLPs) interacting with hACE2-bearing extracellular vesicles (tEVs), showing various intermediate states of the SARS-CoV-2 spike protein (Fig. 4B-E and Supp. Movie 3 of manuscript Marcink et al., 2021).
Sample
Complex: Virus-like particles and extracellular vesicles
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
F32AI152275
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI114736
United States
Citation
Journal: Sci Adv / Year: 2022 Title: Intermediates in SARS-CoV-2 spike-mediated cell entry. Authors: Tara C Marcink / Thomas Kicmal / Emily Armbruster / Zhening Zhang / Gillian Zipursky / Kate L Golub / Mohab Idris / Jonathan Khao / Jennifer Drew-Bear / Gael McGill / Tom Gallagher / Matteo ...Authors: Tara C Marcink / Thomas Kicmal / Emily Armbruster / Zhening Zhang / Gillian Zipursky / Kate L Golub / Mohab Idris / Jonathan Khao / Jennifer Drew-Bear / Gael McGill / Tom Gallagher / Matteo Porotto / Amédée des Georges / Anne Moscona / Abstract: SARS-CoV-2 cell entry is completed after viral spike (S) protein-mediated membrane fusion between viral and host cell membranes. Stable prefusion and postfusion S structures have been resolved by ...SARS-CoV-2 cell entry is completed after viral spike (S) protein-mediated membrane fusion between viral and host cell membranes. Stable prefusion and postfusion S structures have been resolved by cryo-electron microscopy and cryo-electron tomography, but the refolding intermediates on the fusion pathway are transient and have not been examined. We used an antiviral lipopeptide entry inhibitor to arrest S protein refolding and thereby capture intermediates as S proteins interact with hACE2 and fusion-activating proteases on cell-derived target membranes. Cryo-electron tomography imaged both extended and partially folded intermediate states of S2, as well as a novel late-stage conformation on the pathway to membrane fusion. The intermediates now identified in this dynamic S protein-directed fusion provide mechanistic insights that may guide the design of CoV entry inhibitors.
Download / File: emd_24601.map.gz / Format: CCP4 / Size: 702.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotation
Tomogram of SARS-CoV-2 spike-bearing virus-like particles (VLPs) interacting with hACE2-bearing extracellular vesicles (tEVs), showing various intermediate states of the SARS-CoV-2 spike protein (Fig. 4B-E and Supp. Movie 3 of manuscript Marcink et al., 2021).
Voxel size
X=Y=Z: 6.484 Å
Density
Minimum - Maximum
-1679.0 - 687.0
Average (Standard dev.)
87.55251 (±38.75694)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-208
209
-200
Dimensions
1440
1023
250
Spacing
1023
1440
250
Cell
A: 6633.1323 Å / B: 9336.96 Å / C: 1621.0 Å α=β=γ: 90.0 °
-
Supplemental data
-
Sample components
-
Entire : Virus-like particles and extracellular vesicles
Entire
Name: Virus-like particles and extracellular vesicles
Components
Complex: Virus-like particles and extracellular vesicles
Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 300.0 nm
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Sectioning
Other: NO SECTIONING
Fiducial marker
Manufacturer: Sigma Aldrich / Diameter: 5 nm
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recording
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.8 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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