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- EMDB-60524: Cryo-EM structure of MRCoV RBD in complex with mink ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-60524
TitleCryo-EM structure of MRCoV RBD in complex with mink ACE2
Map data
Sample
  • Complex: MRCoV RBD in complex with mink ACE2
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeogale vison HKU5-related coronavirus / mink ACE2 / Complex / VIRAL PROTEIN/HYDROLASE / 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 speciesNeogale vison (American mink) / Bat coronavirus HKU5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsJi W / Zhang S
Funding support China, 1 items
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, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60524.png

Downloads & links

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Map

FileDownload / File: emd_60524.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 280 pix.
= 187.04 Å		0.67 Å/pix.
x 280 pix.
= 187.04 Å		0.67 Å/pix.
x 280 pix.
= 187.04 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-2.0590618 - 3.0285144
Average (Standard dev.)0.0014256198 (±0.08146318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 187.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60524_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60524_half_map_2.map
Projections & Slices
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Sample components

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Entire : MRCoV RBD in complex with mink ACE2

EntireName: MRCoV RBD in complex with mink ACE2
Components
  • Complex: MRCoV RBD in complex with mink ACE2
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: MRCoV RBD in complex with mink ACE2

SupramoleculeName: MRCoV RBD in complex with mink ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Neogale vison (American mink)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bat coronavirus HKU5
Molecular weightTheoretical: 25.879896 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: EASPRGEFIE QSTAKECDFS PMLQGTPPPI YDFKRLVFTN CNYNLTKLLN LFQVSEFSCH QVSPSSLATG CYSSLTVDYF AYPTSMSSY LQPGFAGEIV KFNYKQDFSS PTCRVLATVP SNLTTITKPS NYVHLTECYK GTAYGKNYLY NAPGGYTPCL S LASSGFSS ...String:
EASPRGEFIE QSTAKECDFS PMLQGTPPPI YDFKRLVFTN CNYNLTKLLN LFQVSEFSCH QVSPSSLATG CYSSLTVDYF AYPTSMSSY LQPGFAGEIV KFNYKQDFSS PTCRVLATVP SNLTTITKPS NYVHLTECYK GTAYGKNYLY NAPGGYTPCL S LASSGFSS DRQSHRQQLS DGYLVTTGSV YAVNGNLQMA FIISVQYGTD TNSVCPMQAL RNDTSIEDKL DTCVQY

UniProtKB: Spike glycoprotein

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Macromolecule #2: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Neogale vison (American mink)
Molecular weightTheoretical: 69.733297 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: STTEDLAKTF LEKFNYEAEE LSYQNSLASW NYNTNITDEN IQKMNIAGAK WSAFYEEESQ HAKTYPLEEI QDPIIKRQLR ALQQSGSSV LSADKRERLN TILNAMSTIY STGKACNPNN PQECLLLEPG LDDIMENSKD YNERLWAWEG WRSEVGKQLR P LYEEYVAL ...String:
STTEDLAKTF LEKFNYEAEE LSYQNSLASW NYNTNITDEN IQKMNIAGAK WSAFYEEESQ HAKTYPLEEI QDPIIKRQLR ALQQSGSSV LSADKRERLN TILNAMSTIY STGKACNPNN PQECLLLEPG LDDIMENSKD YNERLWAWEG WRSEVGKQLR P LYEEYVAL KNEMARANNY EDYGDYWRGD YEEEWADGYN YSRNQLIEDV EHTFTQIKPL YEHLHAYVRA KLMDAYPSRI SP TGCLPAH LLGDMWGRFW TNLYPLMVPF GQKPNIDVTD AMVNQSWDAR RIFKEAEKFF VSVGLPNMTE GFWQNSMLTE PGD NRKVVC HPTAWDLGKH DFRIKMCTKV TMDDFLTAHH EMGHIQYDMA YAAQPFLLRN GANEGFHEAV GEIMSLSAAT PNHL KNIGL LPPDFSEDSE TDINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKEQW MQKWWEMKRD IVGVVEPLPH DETYC DPAA LFHVANDYSF IRYYTRTIYQ FQFQEALCQI AKHEGPLYKC DISNSREAGQ KLHEMLSLGR SKPWTFALER VVGAKT MDV RPLLNYFEPL FTWLKEQNRN SFVGWNTDWS PYAD

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1182781
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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