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Yorodumi- PDB-7y6d: Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y6d | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD | ||||||
Components | Spike glycoprotein | ||||||
Keywords | VIRAL PROTEIN / trimer | ||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.39 Å | ||||||
Authors | Xu, J. / Song, Y. / Li, S. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y6d.cif.gz | 555.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y6d.ent.gz | 452.6 KB | Display | PDB format |
PDBx/mmJSON format | 7y6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y6d_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7y6d_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7y6d_validation.xml.gz | 89.4 KB | Display | |
Data in CIF | 7y6d_validation.cif.gz | 135.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/7y6d ftp://data.pdbj.org/pub/pdb/validation_reports/y6/7y6d | HTTPS FTP |
-Related structure data
Related structure data | 33205MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 141484.719 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: T19R, G142D, L452R, T478K, D614G, P681R, D950N are Variants observed in Delta. Source: (natural) Severe acute respiratory syndrome coronavirus 2 Variant: Delta variant / References: UniProt: P0DTC2 #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 | N | |
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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 |
-Sample preparation
Component | Name: Severe acute respiratory syndrome coronavirus 2 / Type: VIRUS / Entity ID: #1 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION | |||||||||||||||||||||||||
Natural host | Organism: Homo sapiens | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: NITROGEN |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 25851 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Details: CTFs are applied to the projections of the map during 3D classification and 3D refinement. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 674792 Details: Initial micrographs were deconvolved using Warp, and 7,950 spikes were manually picked from 474 micrographs for training Topaz neural network. The trained Topaz neural network was used to ...Details: Initial micrographs were deconvolved using Warp, and 7,950 spikes were manually picked from 474 micrographs for training Topaz neural network. The trained Topaz neural network was used to automatically pick the spikes. 674,792 particles were auto-picked by Topaz. | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45252 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 118.79 / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building |
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