7TF1

Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein (focused refinement of RBD)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants.

Saville, J.W.Mannar, D.Zhu, X.Srivastava, S.S.Berezuk, A.M.Demers, J.P.Zhou, S.Tuttle, K.S.Sekirov, I.Kim, A.Li, W.Dimitrov, D.S.Subramaniam, S.

(2022) Nat Commun 13: 742-742

  • DOI: https://doi.org/10.1038/s41467-022-28324-6
  • Primary Citation of Related Structures:  
    7TEW, 7TEX, 7TEY, 7TEZ, 7TF0, 7TF1, 7TF2, 7TF3, 7TF4, 7TF5

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C, D, E
A, B, C, D, E, F
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 15 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth B]
J [auth B]
K [auth C]
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth D],
N [auth D],
O [auth E],
P [auth E],
Q [auth F],
R [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canada Excellence Research Chair AwardPrecision Cancer Drug Design
Other governmentCOVID-19 research

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release