8T21 | pdb_00008t21

Cryo-EM structure of mink variant Y453F trimeric spike protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8T21

This is version 1.1 of the entry. See complete history

Literature

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS-CoV-2.

Ahn, H.Calderon, B.M.Fan, X.Gao, Y.Horgan, N.L.Jiang, N.Blohm, D.S.Hossain, J.Rayyan, N.W.K.Osman, S.H.Lin, X.Currier, M.Steel, J.Wentworth, D.E.Zhou, B.Liang, B.

(2023) J Med Virol 95: e29163-e29163

  • DOI: https://doi.org/10.1002/jmv.29163
  • Primary Citation Related Structures: 
    8T20, 8T21, 8T22, 8T23, 8T25, 8TAZ

  • PubMed Abstract: 

    Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) enters the host cell by binding to angiotensin-converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS-CoV-2 viruses impact species specificity. Reverse zoonoses led to SARS-CoV-2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink-associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio-layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink-derived S glycoproteins of SARS-CoV-2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo-electron microscopy (cryo-EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor-binding domain (RBD) of the S glycoprotein in a "down" position, approximately 34° lower than previously reported "up" RBD. Finally, we compared residue interactions in the S-ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS-CoV-2 entry.


  • Organizational Affiliation
    • Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.

Macromolecule Content 

  • Total Structure Weight: 420.73 kDa 
  • Atom Count: 23,430 
  • Modeled Residue Count: 3,003 
  • Deposited Residue Count: 3,807 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,269Severe acute respiratory syndrome coronavirus 2Mutation(s): 10 
UniProt
Find proteins for A0A6H1PJZ3 (Severe acute respiratory syndrome coronavirus 2)
Explore A0A6H1PJZ3 
Go to UniProtKB:  A0A6H1PJZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6H1PJZ3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary