9MV0 | pdb_00009mv0

Structure of HKU5 spike C-terminal domain in complex with ACE2 from Pipistrellus abramus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

HKU5 bat merbecoviruses engage bat and mink ACE2 as entry receptors.

Madel Alfajaro, M.Keeler, E.L.Li, N.Catanzaro, N.J.Teng, I.T.Zhao, Z.Grunst, M.W.Yount, B.Schafer, A.Wang, D.Kim, A.S.Synowiec, A.Pena-Hernandez, M.A.Zepeda, S.Arinola, R.Kaur, R.Menasche, B.L.Wei, J.Russell, G.A.Huck, J.Song, J.Ring, A.Iwasaki, A.Jangra, R.K.Lee, S.Martinez, D.R.Mothes, W.Uchil, P.D.Doench, J.G.Spaulding, A.B.Baric, R.S.Serebryannyy, L.Tsybovsky, Y.Zhou, T.Douek, D.C.Wilen, C.B.

(2025) Nat Commun 16: 6822-6822

  • DOI: https://doi.org/10.1038/s41467-025-61583-7
  • Primary Citation of Related Structures:  
    9MV0

  • PubMed Abstract: 

    Identifying receptors for bat coronaviruses is critical for spillover risk assessment, countermeasure development, and pandemic preparedness. While Middle East respiratory syndrome coronavirus (MERS-CoV) uses DPP4 for entry, the receptors of many MERS-related betacoronaviruses remain unknown. The bat merbecovirus HKU5 was previously shown to have an entry restriction in human cells. Using both pseudotyped and full-length virus, we show that HKU5 uses Pipistrellus abramus bat ACE2 but not human ACE2 or DPP4 as a receptor. Cryo-electron microscopy analysis of the virus-receptor complex and structure-guided mutagenesis reveal a spike and ACE2 interaction that is distinct from other ACE2-using coronaviruses. MERS-CoV vaccine sera poorly neutralize HKU5 informing pan-merbecovirus vaccine design. Notably, HKU5 can also engage American mink and stoat ACE2, revealing mustelids as potential intermediate hosts. These findings highlight the versatility of merbecovirus receptor use and underscore the need for continued surveillance of bat and mustelid species.


  • Organizational Affiliation
    • Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme
A, C
803Pipistrellus abramusMutation(s): 0 
EC: 3.4
UniProt
Find proteins for C7ECT9 (Pipistrellus abramus)
Explore C7ECT9 
Go to UniProtKB:  C7ECT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7ECT9
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
B, D
1,352Pipistrellus bat coronavirus HKU5Mutation(s): 0 
Gene Names: S2
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
Sequence Annotations
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  • 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
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTPHENIX1.21.1_5286
MODEL REFINEMENTISOLDE

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Data collection, Database references