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TitleEvolution of the SARS-CoV-2 spike protein in the human host.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 1178, Year 2022
Publish dateMar 4, 2022
AuthorsAntoni G Wrobel / Donald J Benton / Chloë Roustan / Annabel Borg / Saira Hussain / Stephen R Martin / Peter B Rosenthal / John J Skehel / Steven J Gamblin /
PubMed AbstractRecently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have ...Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (Alpha) and B.1.351 (Beta) variants to better understand the evolution of the virus in humans. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. Each variant spike has acquired other key changes in structure that likely impact virus pathogenesis. The spike from the Alpha variant is more stable against disruption upon binding ACE2 receptor than all other spikes studied. This feature is linked to the acquisition of a more basic substitution at the S1-S2 furin site (also observed for the variants of concern Delta, Kappa, and Omicron) which allows for near-complete cleavage. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. Our observations suggest ways these viruses have evolved to achieve greater transmissibility in humans.
External linksNat Commun / PubMed:35246509 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 4.1 Å
Structure data

EMDB-14225, PDB-7r0z:
Dissociated S1 domain of Alpha Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-14226, PDB-7r10:
Dissociated S1 domain of Alpha Variant SARS-CoV-2 Spike bound to ACE2
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-14227, PDB-7r11:
Dissociated S1 domain of Beta Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-14228, PDB-7r12:
Dissociated S1 domain of Mink Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-14229, PDB-7r13:
Alpha Variant SARS-CoV-2 Spike in Closed conformation
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-14230, PDB-7r14:
Alpha Variant SARS-CoV-2 Spike with 1 Erect RBD
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-14231, PDB-7r15:
Alpha Variant SARS-CoV-2 Spike with 2 Erect RBDs
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-14232, PDB-7r16:
Beta Variant SARS-CoV-2 Spike with 1 Erect RBD
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-14233, PDB-7r17:
Beta Variant SARS-CoV-2 Spike with 2 Erect RBDs
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-14234, PDB-7r18:
Mink Variant SARS-CoV-2 Spike in Closed conformation
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-14235, PDB-7r19:
Mink Variant SARS-CoV-2 Spike with 2 Erect RBDs
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-14236, PDB-7r1a:
Furin Cleaved Alpha Variant SARS-CoV-2 Spike in complex with 3 ACE2
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-14237, PDB-7r1b:
Mink Variant SARS-CoV-2 Spike with 1 Erect RBD
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / Spike / SARS-CoV-2

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