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- EMDB-49092: Structure of the Rattus norvegicus ACE2 receptor bound HsItaly201... -

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Entry
Database: EMDB / ID: EMD-49092
TitleStructure of the Rattus norvegicus ACE2 receptor bound HsItaly2011 RBD complex
Map data
Sample
  • Complex: R.nor ACE2 receptor bound HsItaly2011 RBD complex
    • Protein or peptide: Angiotensin-converting enzyme 2
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water
KeywordsHKU25 coronaviruses / MERSr-CoV / Spike glycoprotein / fusion protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / inhibitor / VIRAL PROTEIN-HYDROLASE complex / HYDROLASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction ...Metabolism of Angiotensinogen to Angiotensins / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / transporter activator activity / carboxypeptidase activity / angiotensin maturation / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / virus receptor activity / endopeptidase activity / entry receptor-mediated virion attachment to host cell / 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 / symbiont entry into host cell / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular region / metal ion binding / identical protein binding / membrane / plasma 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. / Neutral zinc metallopeptidases, zinc-binding region signature. / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Trp-Asp (WD) repeats signature.
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesMerbecovirus / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsPark YJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: ACE2 utilization of HKU25 clade MERS-related coronaviruses with broad geographic distribution.
Authors: Chen Liu / Young-Jun Park / Cheng-Bao Ma / Cameron Stuart / Risako Gen / Yu-Cheng Sun / Xiao Yang / Mei-Yi Lin / Qing Xiong / Jun-Yu Si / Peng Liu / David Veesler / Huan Yan /
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 ...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.
History
DepositionFeb 5, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49092.png

Downloads & links

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Map

FileDownload / File: emd_49092.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 320 pix.
= 320.352 Å		1 Å/pix.
x 320 pix.
= 320.352 Å		1 Å/pix.
x 320 pix.
= 320.352 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0011 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-3.0131364 - 4.901137
Average (Standard dev.)0.000054983906 (±0.071370184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 320.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49092_additional_1.map
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Half map: #2

Fileemd_49092_half_map_1.map
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Half map: #1

Fileemd_49092_half_map_2.map
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Sample components

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Entire : R.nor ACE2 receptor bound HsItaly2011 RBD complex

EntireName: R.nor ACE2 receptor bound HsItaly2011 RBD complex
Components
  • Complex: R.nor ACE2 receptor bound HsItaly2011 RBD complex
    • Protein or peptide: Angiotensin-converting enzyme 2
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: R.nor ACE2 receptor bound HsItaly2011 RBD complex

SupramoleculeName: R.nor ACE2 receptor bound HsItaly2011 RBD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Merbecovirus / Strain: HsItaly2011

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Macromolecule #1: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 88.709758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSSCWLLLS LVAVATAQSL IEEKAESFLN KFNQEAEDLS YQSSLASWNY NTNITEENAQ KMNEAAAKWS AFYEEQSKIA QNFSLQEIQ NATIKRQLKA LQQSGSSALS PDKNKQLNTI LNTMSTIYST GKVCNSMNPQ ECFLLEPGLD EIMATSTDYN R RLWAWEGW ...String:
MSSSCWLLLS LVAVATAQSL IEEKAESFLN KFNQEAEDLS YQSSLASWNY NTNITEENAQ KMNEAAAKWS AFYEEQSKIA QNFSLQEIQ NATIKRQLKA LQQSGSSALS PDKNKQLNTI LNTMSTIYST GKVCNSMNPQ ECFLLEPGLD EIMATSTDYN R RLWAWEGW RAEVGKQLRP LYEEYVVLKN EMARANNYED YGDYWRGDYE AEGVEGYNYN RNQLIEDVEN TFKEIKPLYE QL HAYVRTK LMEVYPSYIS PTGCLPAHLL GDMWGRFWTN LYPLTTPFLQ KPNIDVTDAM VNQSWDAERI FKEAEKFFVS VGL PQMTPG FWTNSMLTEP GDDRKVVCHP TAWDLGHGDF RIKMCTKVTM DNFLTAHHEM GHIQYDMAYA KQPFLLRNGA NEGF HEAVG EIMSLSAATP KHLKSIGLLP SNFQEDNETE INFLLKQALT IVGTLPFTYM LEKWRWMVFQ DKIPREQWTK KWWEM KREI VGVVEPLPHD ETYCDPASLF HVSNDYSFIR YYTRTIYQFQ FQEALCQAAK HDGPLHKCDI SNSTEAGQKL LNMLSL GNS GPWTLALENV VGSRNMDVKP LLNYFQPLFV WLKEQNRNST VGWSTDWSPY ADQSIKVRIS LKSALGKNAY EWTDNEM YL FRSSVAYAMR EYFSREKNQT VPFGEADVWV SDLKPRVSFN FFVTSPKNVS DIIPRSEVEE AIRMSRGRIN DIFGLNDN S LEFLGIYPTL KPPYEPPVTI GLNDIFEAQK IEWHEGGSHH HHHHHH

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Merbecovirus / Strain: HsItaly2011
Molecular weightTheoretical: 29.871674 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTECDFSKLF KAAPPQIYNF SRLVFTNCNY NLTKLLSLFH VSEFSCHQVS PSALASGCY SSLTVDYFAY PLYLASYLQQ GSTGEIAQYN YKQDFSNPTC RILASVPANV SIPKPDKYIW LSQCYSFSAY S GDVPHYVL ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTECDFSKLF KAAPPQIYNF SRLVFTNCNY NLTKLLSLFH VSEFSCHQVS PSALASGCY SSLTVDYFAY PLYLASYLQQ GSTGEIAQYN YKQDFSNPTC RILASVPANV SIPKPDKYIW LSQCYSFSAY S GDVPHYVL PGQYTPCLYL TSSGFDNSYQ TNRDFQNKMA ATGVISSMTD NLQMAFVISV QYGTDTNSVC PMQALRLVPR GS SSGGSGL NDIFEAQKIE WHEGGSHHHH HHHH

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 110 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.2 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 831432
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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