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Yorodumi- EMDB-32825: Negative stain volume of the mono-GlcNAc-decorated SARS-CoV-2 Spike -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32825 | |||||||||
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Title | Negative stain volume of the mono-GlcNAc-decorated SARS-CoV-2 Spike | |||||||||
Map data | negative stain volume of the mono-GlcNAc-decorated SARS-CoV-2 Spike | |||||||||
Sample |
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Function / homology | Function and homology information 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 / membrane fusion / Attachment and Entry / 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 | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 14.5 Å | |||||||||
Authors | Chen X / Huang H-Y | |||||||||
Funding support | Taiwan, 1 items
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Citation | Journal: Sci Transl Med / Year: 2022 Title: Vaccination with SARS-CoV-2 spike protein lacking glycan shields elicits enhanced protective responses in animal models. Authors: Han-Yi Huang / Hsin-Yu Liao / Xiaorui Chen / Szu-Wen Wang / Cheng-Wei Cheng / Md Shahed-Al-Mahmud / Yo-Min Liu / Arpita Mohapatra / Ting-Hua Chen / Jennifer M Lo / Yi-Min Wu / Hsiu-Hua Ma / ...Authors: Han-Yi Huang / Hsin-Yu Liao / Xiaorui Chen / Szu-Wen Wang / Cheng-Wei Cheng / Md Shahed-Al-Mahmud / Yo-Min Liu / Arpita Mohapatra / Ting-Hua Chen / Jennifer M Lo / Yi-Min Wu / Hsiu-Hua Ma / Yi-Hsuan Chang / Ho-Yang Tsai / Yu-Chi Chou / Yi-Ping Hsueh / Ching-Yen Tsai / Pau-Yi Huang / Sui-Yuan Chang / Tai-Ling Chao / Han-Chieh Kao / Ya-Min Tsai / Yen-Hui Chen / Chung-Yi Wu / Jia-Tsrong Jan / Ting-Jen Rachel Cheng / Kuo-I Lin / Che Ma / Chi-Huey Wong / Abstract: A major challenge to end the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is to develop a broadly protective vaccine that elicits long-term immunity. As the key ...A major challenge to end the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is to develop a broadly protective vaccine that elicits long-term immunity. As the key immunogen, the viral surface spike (S) protein is frequently mutated, and conserved epitopes are shielded by glycans. Here, we revealed that S protein glycosylation has site-differential effects on viral infectivity. We found that S protein generated by lung epithelial cells has glycoforms associated with increased infectivity. Compared to the fully glycosylated S protein, immunization of S protein with N-glycans trimmed to the mono-GlcNAc-decorated state (S) elicited stronger immune responses and better protection for human angiotensin-converting enzyme 2 (hACE2) transgenic mice against variants of concern (VOCs). In addition, a broadly neutralizing monoclonal antibody was identified from S-immunized mice that could neutralize wild-type SARS-CoV-2 and VOCs with subpicomolar potency. Together, these results demonstrate that removal of glycan shields to better expose the conserved sequences has the potential to be an effective and simple approach for developing a broadly protective SARS-CoV-2 vaccine. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_32825.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-32825-v30.xml emd-32825.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_32825.png | 40.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32825 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32825 | HTTPS FTP |
-Validation report
Summary document | emd_32825_validation.pdf.gz | 352.7 KB | Display | EMDB validaton report |
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Full document | emd_32825_full_validation.pdf.gz | 352.2 KB | Display | |
Data in XML | emd_32825_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_32825_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32825 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32825 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32825.map.gz / Format: CCP4 / Size: 4.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | negative stain volume of the mono-GlcNAc-decorated SARS-CoV-2 Spike | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 Spike
Entire | Name: SARS-CoV-2 Spike |
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Components |
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-Supramolecule #1: SARS-CoV-2 Spike
Supramolecule | Name: SARS-CoV-2 Spike / type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293 |
Molecular weight | Experimental: 430 kDa/nm |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Staining | Type: NEGATIVE / Material: uranyl acetate / Details: 1% |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Number grids imaged: 1 / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |