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Yorodumi- PDB-7e9t: Nanometer resolution in situ structure of SARS-CoV-2 post-fusion spike -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e9t | ||||||
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Title | Nanometer resolution in situ structure of SARS-CoV-2 post-fusion spike | ||||||
Components | Spike protein S2 | ||||||
Keywords | VIRUS / SARS-CoV-2 / in situ / post-fusion / spike / cryo-STA | ||||||
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 / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 10.9 Å | ||||||
Authors | Zhu, Y. / Tai, L. / Zhu, G. / Yin, G. / Sun, F. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein. Authors: Linhua Tai / Guoliang Zhu / Minnan Yang / Lei Cao / Xiaorui Xing / Guoliang Yin / Chun Chan / Chengfeng Qin / Zihe Rao / Xiangxi Wang / Fei Sun / Yun Zhu / Abstract: The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates membrane fusion to allow entry of the viral genome into host cells. To understand its detailed entry ...The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates membrane fusion to allow entry of the viral genome into host cells. To understand its detailed entry mechanism and develop a specific entry inhibitor, in situ structural information on the SARS-CoV-2 spike protein in different states is urgent. Here, by using cryo-electron tomography, we observed both prefusion and postfusion spikes in β-propiolactone-inactivated SARS-CoV-2 virions and solved the in situ structure of the postfusion spike at nanometer resolution. Compared to previous reports, the six-helix bundle fusion core, the glycosylation sites, and the location of the transmembrane domain were clearly resolved. We observed oligomerization patterns of the spikes on the viral membrane, likely suggesting a mechanism of fusion pore formation. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 7e9t.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e9t.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 7e9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/7e9t ftp://data.pdbj.org/pub/pdb/validation_reports/e9/7e9t | HTTPS FTP |
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-Related structure data
Related structure data | 31037MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 58672.516 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTC2 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: 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: subtomogram averaging |
-Sample preparation
Component | Name: Severe acute respiratory syndrome coronavirus 2SARS-CoV-2 Type: VIRUS / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Details of virus | Empty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy |
Image recording | Electron dose: 3 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5463 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 352 / Num. of volumes extracted: 7869 | ||||||||||||||||||||||||
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