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TitleStructures and receptor binding activities of merbecovirus spike proteins reveal key signatures for human DPP4 adaptation.
Journal, issue, pagesSci Adv, Vol. 11, Issue 28, Page eadv7296, Year 2025
Publish dateJul 11, 2025
AuthorsHang Yuan / Jingjing Wang / Yong Ma / Zimu Li / Xijie Gao / Gul Habib / Banghui Liu / Jing Chen / Jun He / Peng Zhou / Zheng-Li Shi / Xinwen Chen / Xiaoli Xiong /
PubMed AbstractMerbecoviruses from bats, pangolins, and hedgehogs pose significant zoonotic threats, with a limited understanding of receptor binding by their spike (S) proteins. Here, we report cryo-EM structures ...Merbecoviruses from bats, pangolins, and hedgehogs pose significant zoonotic threats, with a limited understanding of receptor binding by their spike (S) proteins. Here, we report cryo-EM structures of GD-BatCoV (BtCoV-422) and SE-PangolinCoV (MjHKU4r-CoV-1) RBDs in complex with human DPP4 (hDPP4). These structures exhibit a substantial offset in their hDPP4 interaction interfaces, revealing a conserved hydrophobic cluster as a convergent signature of DPP4 binding within the MERS-HKU4 clade of merbecoviruses. Structure-guided mutagenesis demonstrates that favorable interactions are distributed across multiple receptor binding motif (RBM) regions, working synergistically to confer high-affinity hDPP4 binding. Swapping of the merbecovirus RBM regions indicate limited plasticity and interchangeability among these regions. In addition, we report cryo-EM structures of six merbecovirus S-trimers. Structure-based phylogenetics suggests that hDPP4-binding merbecoviruses undergo convergent evolution, while ACE2-binding merbecoviruses exhibit diversification in their binding mechanisms. These findings offer critical insights into merbecovirus receptor utilization, providing a structural understanding for future surveillance.
External linksSci Adv / PubMed:40644548 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 3.8 Å
Structure data

61600

9jmf

EMDB-61600, PDB-9jmf:
Cryo-EM structure of SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) S-trimer
Method: EM (single particle) / Resolution: 3.1 Å

61601

9jmg

EMDB-61601, PDB-9jmg:
Cryo-EM structure of EU-HedgehogCoV (Erinaceus/VMC/DEU/2012) S-trimer in a locked-2 conformation
Method: EM (single particle) / Resolution: 3.0 Å

61602

9jmh

EMDB-61602, PDB-9jmh:
Cryo-EM structure of HKU25-BatCoV S-trimer stabilized with 2P and x1 disulfide bond
Method: EM (single particle) / Resolution: 3.0 Å

61603

9jmi

EMDB-61603, PDB-9jmi:
Cryo-EM structure of CN-HedgehogCoV (HKU31/Erinaceus amurensis/China/2014) S-trimer in a locked-2 conformation
Method: EM (single particle) / Resolution: 3.3 Å

61604

9jmj

EMDB-61604, PDB-9jmj:
Cryo-EM structure of the GD-BatCoV (BtCoV/Ii/GD/2014-422) RBD in complex with human DPP4
Method: EM (single particle) / Resolution: 3.4 Å

61606

9jmm

EMDB-61606, PDB-9jmm:
Cryo-EM structure of the SE-PangolinCoV (MjHKU4r-CoV-1) RBD in complex with human DPP4
Method: EM (single particle) / Resolution: 2.8 Å

61607

9jmn

EMDB-61607, PDB-9jmn:
Cryo-EM structure of CN-HedgehogCoV (HKU31/Erinaceus amurensis/China/2014) S-trimer in a locked-1 conformation
Method: EM (single particle) / Resolution: 3.8 Å

61608

9jmo

EMDB-61608, PDB-9jmo:
Cryo-EM structure of Japan-BatCoV (Vs-CoV-1) S-trimer
Method: EM (single particle) / Resolution: 2.8 Å

61609

9jmp

EMDB-61609, PDB-9jmp:
Cryo-EM structure of GD-BatCoV (BtCoV/Ii/GD/2014-422) S-trimer
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-EIC:
LINOLEIC ACID

ChemComp-FOL:
FOLIC ACID

Source
  • coronavirus neoromicia/pml-phe1/rsa/2011
  • enterobacteria phage t4 (virus)
  • betacoronavirus erinaceus/vmc/deu/2012
  • enterobacteria phage t4 (bacteriophage t4) (virus)
  • hypsugo bat coronavirus hku25
  • tequatrovirus t4
  • erinaceus hedgehog coronavirus hku31
  • middle east respiratory syndrome-related coronavirus
  • homo sapiens (human)
  • pangolin coronavirus hku4/p251t/pangolin/2018
  • bat coronavirus
KeywordsVIRAL PROTEIN / spike protein / complex

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