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TitleStructural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 742, Year 2022
Publish dateFeb 8, 2022
AuthorsJames W Saville / Dhiraj Mannar / Xing Zhu / Shanti S Srivastava / Alison M Berezuk / Jean-Philippe Demers / Steven Zhou / Katharine S Tuttle / Inna Sekirov / Andrew Kim / Wei Li / Dimiter S Dimitrov / Sriram Subramaniam /
PubMed AbstractThe Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this ...The Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this study, we assess structural and biochemical aspects of viral fitness for these two variants using cryo-electron microscopy (cryo-EM), ACE2-binding and antibody neutralization analyses. Both variants demonstrate escape of antibodies targeting the N-terminal domain, an important immune hotspot for neutralizing epitopes. Compared to wild-type and Kappa lineages, Delta variant spike proteins show modest increase in ACE2 affinity, likely due to enhanced electrostatic complementarity at the RBD-ACE2 interface, which we characterize by cryo-EM. Unexpectedly, Kappa variant spike trimers form a structural head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation and with unknown biological implications. The combination of increased antibody escape and enhanced ACE2 binding provides an explanation, in part, for the rapid global dominance of the Delta variant.
External linksNat Commun / PubMed:35136050 / PubMed Central
MethodsEM (single particle)
Resolution2.25 - 3.62 Å
Structure data

25853

7tew

EMDB-25853, PDB-7tew:
Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)
Method: EM (single particle) / Resolution: 3.52 Å

25854

7tex

EMDB-25854, PDB-7tex:
Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein in complex with human ACE2
Method: EM (single particle) / Resolution: 3.27 Å

25855

7tey

EMDB-25855, PDB-7tey:
Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein
Method: EM (single particle) / Resolution: 2.25 Å

25856

7tez

EMDB-25856, PDB-7tez:
Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)
Method: EM (single particle) / Resolution: 3.27 Å

25857

7tf0

EMDB-25857, PDB-7tf0:
Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein in complex with human ACE2
Method: EM (single particle) / Resolution: 3.02 Å

25858

7tf1

EMDB-25858, PDB-7tf1:
Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein (focused refinement of RBD)
Method: EM (single particle) / Resolution: 3.57 Å

25859

7tf2

EMDB-25859, PDB-7tf2:
Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein
Method: EM (single particle) / Resolution: 3.62 Å

25860

7tf3

EMDB-25860, PDB-7tf3:
Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484A spike protein
Method: EM (single particle) / Resolution: 2.25 Å

25861

7tf4

EMDB-25861, PDB-7tf4:
Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein (focused refinement of RBD)
Method: EM (single particle) / Resolution: 3.01 Å

25862

7tf5

EMDB-25862, PDB-7tf5:
Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein
Method: EM (single particle) / Resolution: 3.16 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / SARS-CoV-2 / glycoprotein / fusion protein / ACE2

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