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Yorodumi- EMDB-33206: Subtomogram average of SARS-CoV-2 Delta variant prefusion S in cl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33206 | |||||||||
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Title | Subtomogram average of SARS-CoV-2 Delta variant prefusion S in closed conformation. | |||||||||
Map data | SARS-CoV-2 Delta variant prefusion S in closed conformation | |||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.8 Å | |||||||||
Authors | Song Y / Zhang Z / Peng C / Li S | |||||||||
Funding support | China, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: In situ architecture and membrane fusion of SARS-CoV-2 Delta variant. Authors: Yutong Song / Hangping Yao / Nanping Wu / Jialu Xu / Zheyuan Zhang / Cheng Peng / Shibo Li / Weizheng Kong / Yong Chen / Miaojin Zhu / Jiaqi Wang / Danrong Shi / Chongchong Zhao / Xiangyun ...Authors: Yutong Song / Hangping Yao / Nanping Wu / Jialu Xu / Zheyuan Zhang / Cheng Peng / Shibo Li / Weizheng Kong / Yong Chen / Miaojin Zhu / Jiaqi Wang / Danrong Shi / Chongchong Zhao / Xiangyun Lu / Martín Echavarría Galindo / Sai Li / Abstract: Among the current five Variants of Concern, infections caused by SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis ...Among the current five Variants of Concern, infections caused by SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis of elevated pathogenicity using recombinant proteins, the architecture of intact Delta virions remains veiled. Moreover, pieces of molecular evidence for the detailed mechanism of S-mediated membrane fusion are missing. Here, we showed the pleomorphic nature of Delta virions from electron beam inactivated samples and reported the in situ structure and distribution of S on the authentic Delta variant. We also captured the virus-virus fusion events, which provided pieces of structural evidence for Delta's attenuated dependency on cellular factors for fusion activation, and proposed a model of S-mediated membrane fusion. Besides, site-specific glycan analysis revealed increased oligomannose-type glycosylation of native Delta S than that of the WT S. Together, these results disclose distinctive factors of Delta being the most virulent SARS-CoV-2 variant. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33206.map.gz | 344 KB | EMDB map data format | |
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Header (meta data) | emd-33206-v30.xml emd-33206.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33206_fsc.xml | 6.2 KB | Display | FSC data file |
Images | emd_33206.png | 53.8 KB | ||
Others | emd_33206_half_map_1.map.gz emd_33206_half_map_2.map.gz | 14.5 MB 14.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33206 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33206 | HTTPS FTP |
-Validation report
Summary document | emd_33206_validation.pdf.gz | 643.7 KB | Display | EMDB validaton report |
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Full document | emd_33206_full_validation.pdf.gz | 643.3 KB | Display | |
Data in XML | emd_33206_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_33206_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33206 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33206 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33206.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 Delta variant prefusion S in closed conformation | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.72 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33206_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33206_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Severe acute respiratory syndrome coronavirus 2
Entire | Name: Severe acute respiratory syndrome coronavirus 2 |
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Components |
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-Supramolecule #1: Severe acute respiratory syndrome coronavirus 2
Supramolecule | Name: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2697049 Sci species name: Severe acute respiratory syndrome coronavirus 2 Sci species strain: B.1.617.2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 0.213 sec. / Average electron dose: 3.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |