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Yorodumi- PDB-7a4n: Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D61... -
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-Basic information
Entry | Database: PDB / ID: 7a4n | ||||||
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Title | Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P, A942P and V987P)(S-closed trimer) | ||||||
Components | Spike glycoprotein,Fibritin | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / virology / COVID-19 / class I fusion proteins / S glycoprotein / cryo-EM / prefusion / corona | ||||||
Function / homology | Function and homology information virion component / 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 ...virion component / 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 Enterobacteria phage T4 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||
Authors | Rutten, L. / Renault, L.L.R. / Juraszek, J. / Langedijk, J.P.M. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Stabilizing the closed SARS-CoV-2 spike trimer. Authors: Jarek Juraszek / Lucy Rutten / Sven Blokland / Pascale Bouchier / Richard Voorzaat / Tina Ritschel / Mark J G Bakkers / Ludovic L R Renault / Johannes P M Langedijk / Abstract: The trimeric spike (S) protein of SARS-CoV-2 is the primary focus of most vaccine design and development efforts. Due to intrinsic instability typical of class I fusion proteins, S tends to ...The trimeric spike (S) protein of SARS-CoV-2 is the primary focus of most vaccine design and development efforts. Due to intrinsic instability typical of class I fusion proteins, S tends to prematurely refold to the post-fusion conformation, compromising immunogenic properties and prefusion trimer yields. To support ongoing vaccine development efforts, we report the structure-based design of soluble S trimers with increased yields and stabilities, based on introduction of single point mutations and disulfide-bridges. We identify regions critical for stability: the heptad repeat region 1, the SD1 domain and position 614 in SD2. We combine a minimal selection of mostly interprotomeric mutations to create a stable S-closed variant with a 6.4-fold higher expression than the parental construct while no longer containing a heterologous trimerization domain. The cryo-EM structure reveals a correctly folded, predominantly closed pre-fusion conformation. Highly stable and well producing S protein and the increased understanding of S protein structure will support vaccine development and serological diagnostics. | ||||||
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 7a4n.cif.gz | 515.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a4n.ent.gz | 419.7 KB | Display | PDB format |
PDBx/mmJSON format | 7a4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a4n_validation.pdf.gz | 933.1 KB | Display | wwPDB validaton report |
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Full document | 7a4n_full_validation.pdf.gz | 954.1 KB | Display | |
Data in XML | 7a4n_validation.xml.gz | 81.4 KB | Display | |
Data in CIF | 7a4n_validation.cif.gz | 126.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/7a4n ftp://data.pdbj.org/pub/pdb/validation_reports/a4/7a4n | HTTPS FTP |
-Related structure data
Related structure data | 11639MC 7ad1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
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Noncrystallographic symmetry (NCS) | NCS domain:
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