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Open data
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Basic information
Entry | Database: PDB / ID: 7fg7 | |||||||||
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Title | Cryo-EM structure of S protein trimer of SARS-CoV2 | |||||||||
![]() | Spike glycoprotein | |||||||||
![]() | PROTEIN BINDING / Antibody | |||||||||
Function / homology | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å | |||||||||
![]() | Song, C. / Murata, K. / Katayama, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Nasal delivery of single-domain antibody improves symptoms of SARS-CoV-2 infection in an animal model. Authors: Kei Haga / Reiko Takai-Todaka / Yuta Matsumura / Chihong Song / Tomomi Takano / Takuto Tojo / Atsushi Nagami / Yuki Ishida / Hidekazu Masaki / Masayuki Tsuchiya / Toshiki Ebisudani / Shinya ...Authors: Kei Haga / Reiko Takai-Todaka / Yuta Matsumura / Chihong Song / Tomomi Takano / Takuto Tojo / Atsushi Nagami / Yuki Ishida / Hidekazu Masaki / Masayuki Tsuchiya / Toshiki Ebisudani / Shinya Sugimoto / Toshiro Sato / Hiroyuki Yasuda / Koichi Fukunaga / Akihito Sawada / Naoto Nemoto / Kazuyoshi Murata / Takuya Morimoto / Kazuhiko Katayama / ![]() Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the disease COVID-19 can lead to serious symptoms, such as severe pneumonia, in the elderly and those with underlying ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the disease COVID-19 can lead to serious symptoms, such as severe pneumonia, in the elderly and those with underlying medical conditions. While vaccines are now available, they do not work for everyone and therapeutic drugs are still needed, particularly for treating life-threatening conditions. Here, we showed nasal delivery of a new, unmodified camelid single-domain antibody (VHH), termed K-874A, effectively inhibited SARS-CoV-2 titers in infected lungs of Syrian hamsters without causing weight loss and cytokine induction. In vitro studies demonstrated that K-874A neutralized SARS-CoV-2 in both VeroE6/TMPRSS2 and human lung-derived alveolar organoid cells. Unlike other drug candidates, K-874A blocks viral membrane fusion rather than viral attachment. Cryo-electron microscopy revealed K-874A bound between the receptor binding domain and N-terminal domain of the virus S protein. Further, infected cells treated with K-874A produced fewer virus progeny that were less infective. We propose that direct administration of K-874A to the lung could be a new treatment for preventing the reinfection of amplified virus in COVID-19 patients. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.9 KB | Display | ![]() |
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PDB format | ![]() | 164.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 31578MC ![]() 7fg2C ![]() 7fg3C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 141297.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Minor cryo-EM structure of S protein trimer of SARS-CoV2 Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Details of virus | Empty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Mus musculus |
Virus shell | Diameter: 400 nm / Triangulation number (T number): 3 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: amorphous ice |
Vitrification | Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Microscopy | Model: JEOL 2200FS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 45065 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 1578.3 nm / Calibrated defocus max: 4967.2 nm / Cs: 4.2 mm / C2 aperture diameter: 40 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Temperature (max): 77 K / Temperature (min): 76 K |
Image recording | Average exposure time: 5 sec. / Electron dose: 20 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Num. of real images: 102 |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 6.4 µm / Width: 5120 / Height: 3840 / Movie frames/image: 75 / Used frames/image: 2-25 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14235 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 415 / Protocol: FLEXIBLE FIT / Space: REAL |