9N7D | pdb_00009n7d

Structure of the Rattus norvegicus ACE2 receptor bound HsItaly2011 RBD complex

PDB DOI: https://doi.org/10.2210/pdb9N7D/pdb
EM Map EMD-49092: EMDB EMDataResource

Classification: HYDROLASE/VIRAL PROTEIN
Organism(s): Rattus norvegicus, Merbecovirus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-02-05 Released: 2025-08-27
Deposition Author(s): Park, Y.J., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 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

ACE2 utilization of HKU25 clade MERS-related coronaviruses with broad geographic distribution.

Liu, C., Park, Y.J., Ma, C.B., Stuart, C., Gen, R., Sun, Y.C., Yang, X., Lin, M.Y., Xiong, Q., Si, J.Y., Liu, P., Veesler, D., Yan, H.

(2025) bioRxiv

PubMed: 40027745 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/2025.02.19.639017
Primary Citation Related Structures:
9N7D, 9N7E

PubMed Abstract:
Dipeptidyl peptidase-4 (DPP4) is a well-established receptor for several MERS-related coronaviruses (MERSr-CoVs) isolated from humans, camels, pangolins, and bats (1-6). However, the receptor usage of many genetically diverse bat MERSr-CoVs with broad geographical distributions remains poorly understood. Recent studies have identified angiotensin-converting enzyme 2 (ACE2) as an entry receptor for multiple merbecovirus clades. Here, using viral antigen and pseudovirus-based functional assays, we demonstrate that several bat merbecoviruses from the HKU25 clade previously thought to utilize DPP4 (7), employ ACE2 as their functional receptor. Cryo-electron microscopy analysis revealed that HsItaly2011 and VsCoV-a7 recognize ACE2 with a binding mode sharing similarity with that of HKU5 but involving remodeled interfaces and distinct ortholog selectivity, suggesting a common evolutionary origin of ACE2 utilization for these two clades of viruses. EjCoV-3, a strain closely related to the DPP4-using MERSr-CoV BtCoV-422, exhibited relatively broad ACE2 ortholog tropism and could utilize human ACE2 albeit suboptimally. Despite differences in entry mechanisms and spike proteolytic activation compared to MERS-CoV, these viruses remain sensitive to several broadly neutralizing antibodies and entry inhibitors. These findings redefine our understanding of the evolution of receptor usage among MERSr-CoVs and highlight the versatility of ACE2 as a functional receptor for diverse coronaviruses.

Organizational Affiliation

State Key Laboratory of Virology and Biosafety, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China.

Macromolecule Content

Total Structure Weight: 121.45 kDa
Atom Count: 7,246
Modeled Residue Count: 897
Deposited Residue Count: 1,038
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A	767	Rattus norvegicus	Mutation(s): 0 Gene Names: Ace2 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt
Find proteins for Q5EGZ1 (Rattus norvegicus) Explore Q5EGZ1 Go to UniProtKB: Q5EGZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5EGZ1
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A	Go to GlyGen: Q5EGZ1-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	271	Merbecovirus	Mutation(s): 0
UniProt
Find proteins for A3EXD0 (Bat coronavirus HKU5) Explore A3EXD0 Go to UniProtKB: A3EXD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3EXD0
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], K [auth B], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]