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- PDB-7jjj: Structure of SARS-CoV-2 3Q-2P full-length dimers of spike trimers -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jjj | |||||||||
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Title | Structure of SARS-CoV-2 3Q-2P full-length dimers of spike trimers | |||||||||
![]() | Spike glycoprotein![]() | |||||||||
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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 / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bangaru, S. / Turner, H.L. / Ozorowski, G. / Antanasijevic, A. / Ward, A.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. Authors: Sandhya Bangaru / Gabriel Ozorowski / Hannah L Turner / Aleksandar Antanasijevic / Deli Huang / Xiaoning Wang / Jonathan L Torres / Jolene K Diedrich / Jing-Hui Tian / Alyse D Portnoff / ...Authors: Sandhya Bangaru / Gabriel Ozorowski / Hannah L Turner / Aleksandar Antanasijevic / Deli Huang / Xiaoning Wang / Jonathan L Torres / Jolene K Diedrich / Jing-Hui Tian / Alyse D Portnoff / Nita Patel / Michael J Massare / John R Yates / David Nemazee / James C Paulson / Greg Glenn / Gale Smith / Andrew B Ward / ![]() Abstract: Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV- ...Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. We performed cryo-election microscopy and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax, which is based on a full-length spike protein formulated in polysorbate 80 detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared with published spike ectodomain structures. We also observed interactions between the spike trimers, allowing formation of higher-order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen. #1: Journal: bioRxiv / Year: 2020 Title: Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. Authors: Sandhya Bangaru / Gabriel Ozorowski / Hannah L Turner / Aleksandar Antanasijevic / Deli Huang / Xiaoning Wang / Jonathan L Torres / Jolene K Diedrich / Jing-Hui Tian / Alyse D Portnoff / ...Authors: Sandhya Bangaru / Gabriel Ozorowski / Hannah L Turner / Aleksandar Antanasijevic / Deli Huang / Xiaoning Wang / Jonathan L Torres / Jolene K Diedrich / Jing-Hui Tian / Alyse D Portnoff / Nita Patel / Michael J Massare / John R Yates / David Nemazee / James C Paulson / Greg Glenn / Gale Smith / Andrew B Ward / ![]() Abstract: Vaccine efforts against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic are focused on SARS-CoV-2 spike glycoprotein, the primary target ...Vaccine efforts against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared to published spike ectodomain structures. Interestingly, we also observed novel interactions between the spike trimers allowing formation of higher order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen. | |||||||||
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 | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 22354MC ![]() 7jjiC 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: 141176.125 Da / Num. of mol.: 6 / Mutation: R682Q, R683Q, R685Q, K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Cell (production host): sf9 / 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: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: SARS-CoV-2 full-length spike / 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: 7.2 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 11.5 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 5506 |
Image scans | Movie frames/image: 46 |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15411 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |