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- PDB-8zwe: Cryo-EM structure of MRCoV RBD in complex with mink ACE2 -

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Entry
Database: PDB / ID: 8zwe
TitleCryo-EM structure of MRCoV RBD in complex with mink ACE2
Components
  • Angiotensin-converting enzyme
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/HYDROLASE / Neogale vison HKU5-related coronavirus / mink ACE2 / Complex / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular space / metal ion binding / membrane / cytoplasm
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesBat coronavirus HKU5
Neogale vison (American mink)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsJi, W. / Zhang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170158 China
CitationJournal: Nature / Year: 2025
Title: A MERS-CoV-like mink coronavirus uses ACE2 as an entry receptor.
Authors: Ningning Wang / Weiwei Ji / Houqi Jiao / Michael Veit / Ju Sun / Yanjun Wang / Xing Ma / Yu Wang / Yutong Wang / Xin-Xin Li / Xiaoguang Zhang / Jie Chen / Jiayu Wei / Ying Xu / Dawei Guo / ...Authors: Ningning Wang / Weiwei Ji / Houqi Jiao / Michael Veit / Ju Sun / Yanjun Wang / Xing Ma / Yu Wang / Yutong Wang / Xin-Xin Li / Xiaoguang Zhang / Jie Chen / Jiayu Wei / Ying Xu / Dawei Guo / Xiaofeng Zhai / Andres Merits / Chang Li / Félix A Rey / Georgi M Dobrikov / George F Gao / Shuijun Zhang / Yuhai Bi / Shuo Su /
Abstract: Despite accumulating evidence that bat-derived coronaviruses often require intermediate hosts to facilitate transmission to humans, the potential role of fur animals in zoonotic coronavirus ...Despite accumulating evidence that bat-derived coronaviruses often require intermediate hosts to facilitate transmission to humans, the potential role of fur animals in zoonotic coronavirus spillovers has largely been overlooked. Here we report the isolation and characterization of a previously undescribed mink respiratory coronavirus (MRCoV) from farmed minks with pneumonia. Notably, MRCoV uses angiotensin-converting enzyme 2 (ACE2) as an entry receptor and can infect mink, bat, monkey and human cells. Cryo-electron microscopy analyses revealed that the MRCoV receptor-binding domain (RBD) binds to the same interface on ACE2 receptors as the RBD of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) despite structural differences. We identify the key determinants on the RBD of MRCoV and ACE2 that confer efficient binding. HKU5-33S, a bat coronavirus closely related to MRCoV, uses ACE2 of the bat Pipistrellus abramus for cell entry and requires only two amino acid substitutions to adapt to mink ACE2. SARS-CoV-2 protease and polymerase inhibitors potently block MRCoV infection, thereby indicating a potential therapeutic strategy. Collectively, these findings enhance our understanding of coronavirus receptor dynamics and highlight their zoonotic potential. Given the risks posed by fur farms as reservoirs for emerging pathogens, our study underscores the need for enhanced surveillance to mitigate future coronavirus outbreaks.
History
DepositionJun 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0564
Polymers95,6132
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 25879.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat coronavirus HKU5 / Gene: S / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: S4X422
#2: Protein Angiotensin-converting enzyme


Mass: 69733.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neogale vison (American mink) / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: A0A7T0Q2W2, Hydrolases; Acting on peptide bonds (peptidases)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MRCoV RBD in complex with mink ACE2 / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Neogale vison (American mink)
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1182781 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026649
ELECTRON MICROSCOPYf_angle_d0.4949037
ELECTRON MICROSCOPYf_dihedral_angle_d4.179880
ELECTRON MICROSCOPYf_chiral_restr0.039951
ELECTRON MICROSCOPYf_plane_restr0.0041168

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