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Open data
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Basic information
Entry | Database: PDB / ID: 7q1z | |||||||||
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Title | Structure of formaldehyde cross-linked SARS-CoV-2 S glycoprotein | |||||||||
![]() | Spike glycoprotein | |||||||||
![]() | VIRAL PROTEIN / SARS-CoV-2 / glycoprotein / immunization | |||||||||
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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: 3.4 Å | |||||||||
![]() | Sulbaran, G. / Effantin, G. / Schoehn, G. / Weissenhorn, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. Authors: Guidenn Sulbaran / Pauline Maisonnasse / Axelle Amen / Gregory Effantin / Delphine Guilligay / Nathalie Dereuddre-Bosquet / Judith A Burger / Meliawati Poniman / Marloes Grobben / Marlyse ...Authors: Guidenn Sulbaran / Pauline Maisonnasse / Axelle Amen / Gregory Effantin / Delphine Guilligay / Nathalie Dereuddre-Bosquet / Judith A Burger / Meliawati Poniman / Marloes Grobben / Marlyse Buisson / Sebastian Dergan Dylon / Thibaut Naninck / Julien Lemaître / Wesley Gros / Anne-Sophie Gallouët / Romain Marlin / Camille Bouillier / Vanessa Contreras / Francis Relouzat / Daphna Fenel / Michel Thepaut / Isabelle Bally / Nicole Thielens / Franck Fieschi / Guy Schoehn / Sylvie van der Werf / Marit J van Gils / Rogier W Sanders / Pascal Poignard / Roger Le Grand / Winfried Weissenhorn / ![]() ![]() ![]() Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused an ongoing global health crisis. Here, we present as a vaccine candidate synthetic SARS-CoV-2 spike (S) ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused an ongoing global health crisis. Here, we present as a vaccine candidate synthetic SARS-CoV-2 spike (S) glycoprotein-coated lipid vesicles that resemble virus-like particles. Soluble S glycoprotein trimer stabilization by formaldehyde cross-linking introduces two major inter-protomer cross-links that keep all receptor-binding domains in the "down" conformation. Immunization of cynomolgus macaques with S coated onto lipid vesicles (S-LVs) induces high antibody titers with potent neutralizing activity against the vaccine strain, Alpha, Beta, and Gamma variants as well as T helper (Th)1 CD4-biased T cell responses. Although anti-receptor-binding domain (RBD)-specific antibody responses are initially predominant, the third immunization boosts significant non-RBD antibody titers. Challenging vaccinated animals with SARS-CoV-2 shows a complete protection through sterilizing immunity, which correlates with the presence of nasopharyngeal anti-S immunoglobulin G (IgG) and IgA titers. Thus, the S-LV approach is an efficient and safe vaccine candidate based on a proven classical approach for further development and clinical testing. #1: ![]() Title: Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. Authors: Guidenn Sulbaran / Pauline Maisonnasse / Axelle Amen / Gregory Effantin / Delphine Guilligay / Nathalie Dereuddre-Bosquet / Judith A Burger / Meliawati Poniman / Marloes Grobben / Marlyse ...Authors: Guidenn Sulbaran / Pauline Maisonnasse / Axelle Amen / Gregory Effantin / Delphine Guilligay / Nathalie Dereuddre-Bosquet / Judith A Burger / Meliawati Poniman / Marloes Grobben / Marlyse Buisson / Sebastian Dergan Dylon / Thibaut Naninck / Julien Lemaître / Wesley Gros / Anne-Sophie Gallouët / Romain Marlin / Camille Bouillier / Vanessa Contreras / Francis Relouzat / Daphna Fenel / Michel Thepaut / Isabelle Bally / Nicole Thielens / Franck Fieschi / Guy Schoehn / Sylvie van der Werf / Marit J van Gils / Rogier W Sanders / Pascal Poignard / Roger Le Grand / Winfried Weissenhorn / ![]() ![]() ![]() Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused an ongoing global health crisis. Here, we present as a vaccine candidate synthetic SARS-CoV-2 spike (S) ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused an ongoing global health crisis. Here, we present as a vaccine candidate synthetic SARS-CoV-2 spike (S) glycoprotein-coated lipid vesicles that resemble virus-like particles. Soluble S glycoprotein trimer stabilization by formaldehyde cross-linking introduces two major inter-protomer cross-links that keep all receptor-binding domains in the "down" conformation. Immunization of cynomolgus macaques with S coated onto lipid vesicles (S-LVs) induces high antibody titers with potent neutralizing activity against the vaccine strain, Alpha, Beta, and Gamma variants as well as T helper (Th)1 CD4-biased T cell responses. Although anti-receptor-binding domain (RBD)-specific antibody responses are initially predominant, the third immunization boosts significant non-RBD antibody titers. Challenging vaccinated animals with SARS-CoV-2 shows a complete protection through sterilizing immunity, which correlates with the presence of nasopharyngeal anti-S immunoglobulin G (IgG) and IgA titers. Thus, the S-LV approach is an efficient and safe vaccine candidate based on a proven classical approach for further development and clinical testing. #2: ![]() Title: Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. Authors: Sulbaran, G. / Effantin, G. / Schoehn, G. / Weissenhorn, W. | |||||||||
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 | ![]() | 532.5 KB | Display | ![]() |
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PDB format | ![]() | 445.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 77.6 KB | Display | |
Data in CIF | ![]() | 109.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13776MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 142399.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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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: Trimer of the SARS_CoV-2 S glycoprotein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126719 / Symmetry type: POINT |