9E0I | pdb_00009e0i

Structure of the HKU5-19s RBD bound to the Bos taurus ACE2 receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Resolution: 2.40 Å
  • Resolution: 2.40 Å
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses.

Park, Y.J.Liu, C.Lee, J.Brown, J.T.Ma, C.B.Liu, P.Gen, R.Xiong, Q.Zepeda, S.K.Stewart, C.Addetia, A.Craig, C.J.Tortorici, M.A.Alshukairi, A.N.Starr, T.N.Yan, H.Veesler, D.

(2025) Cell 188: 1711-1728.e21

  • DOI: https://doi.org/10.1016/j.cell.2024.12.032
  • Primary Citation of Related Structures:  
    9D32, 9E0I, 9EA0, 9EH8

  • PubMed Abstract: 

    DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity of ACE2 utilization among merbecoviruses and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. We defined the molecular determinants of receptor species tropism and identified a single amino acid mutation enabling HKU5 to utilize human ACE2, providing proof of principle for machine-learning-assisted outbreak preparedness. We show that MERS-CoV and HKU5 have markedly distinct antigenicity and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution, as several merbecovirus clades independently evolved ACE2 utilization, and pave the way for developing countermeasures against viruses poised for human emergence.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2766Bos taurusMutation(s): 0 
Gene Names: ACE2
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt
Find proteins for Q58DD0 (Bos taurus)
Explore Q58DD0 
Go to UniProtKB:  Q58DD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58DD0
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein267Pipistrellus bat coronavirus HKU5Mutation(s): 0 
UniProt
Find proteins for A3EXD0 (Bat coronavirus HKU5)
Explore A3EXD0 
Go to UniProtKB:  A3EXD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3EXD0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Resolution: 2.40 Å
  • Resolution: 2.40 Å
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI158186

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection, Database references