+Open data
-Basic information
Entry | Database: PDB / ID: 7wgz | ||||||
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Title | SARS-CoV-2 spike glycoprotein trimer in open state | ||||||
Components | Spike glycoprotein | ||||||
Keywords | VIRAL PROTEIN | ||||||
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: 4.5 Å | ||||||
Authors | Zhu, Y. / Tai, L. / Yin, G. / Sun, F. | ||||||
Funding support | 1items
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Citation | Journal: Cell Discov / Year: 2022 Title: Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies Authors: Zhao, M.M. / Zhu, Y. / Zhang, L. / Zhong, G. / Tai, L. / Liu, S. / Yin, G. / Lu, J. / He, Q. / Li, M.J. / Zhao, R.X. / Wang, H. / Huang, W. / Fan, C. / Shuai, L. / Wen, Z. / Wang, C. / He, X. ...Authors: Zhao, M.M. / Zhu, Y. / Zhang, L. / Zhong, G. / Tai, L. / Liu, S. / Yin, G. / Lu, J. / He, Q. / Li, M.J. / Zhao, R.X. / Wang, H. / Huang, W. / Fan, C. / Shuai, L. / Wen, Z. / Wang, C. / He, X. / Chen, Q. / Liu, B. / Xiong, X. / Bu, Z. / Wang, Y. / Sun, F. / Yang, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wgz.cif.gz | 514.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wgz.ent.gz | 404.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wgz_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7wgz_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7wgz_validation.xml.gz | 81.9 KB | Display | |
Data in CIF | 7wgz_validation.cif.gz | 123.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wgz ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wgz | HTTPS FTP |
-Related structure data
Related structure data | 32493MC 7wgvC 7wgxC 7wgyC 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: 133656.984 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / 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 | Has protein modification | Y | |
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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: SARS-CoV-2 Spike Glycoprotein trimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293T |
Buffer solution | pH: 5.5 |
Specimen | Conc.: 2 mg/ml / 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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13523 / Symmetry type: POINT |