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- EMDB-48650: Structure of HKU5 spike C-terminal domain in complex with ACE2 fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-48650
TitleStructure of HKU5 spike C-terminal domain in complex with ACE2 from Pipistrellus abramus
Map data
Sample
  • Complex: ACE2-ACT66266.1 in complex with HKU5-CTD (ABN10875)
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsImmune system / ACE2 / bat coronavirus / merbecovirus / HKU5 / VIRAL PROTEIN
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
Spike glycoprotein / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesPipistrellus abramus bat coronavirus HKU5-related / Pipistrellus abramus (Japanese house bat) / Pipistrellus bat coronavirus HKU5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLi N / Tsybovsky Y / Teng I / Zhou T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2025
Title: HKU5 bat merbecoviruses engage bat and mink ACE2 as entry receptors.
Authors: Mia Madel Alfajaro / Emma L Keeler / Ning Li / Nicholas J Catanzaro / I-Ting Teng / Zhe Zhao / Michael W Grunst / Boyd Yount / Alexandra Schäfer / Danyi Wang / Arthur S Kim / Aleksandra ...Authors: Mia Madel Alfajaro / Emma L Keeler / Ning Li / Nicholas J Catanzaro / I-Ting Teng / Zhe Zhao / Michael W Grunst / Boyd Yount / Alexandra Schäfer / Danyi Wang / Arthur S Kim / Aleksandra Synowiec / Mario A Peña-Hernández / Samantha Zepeda / Ridwan Arinola / Ramandeep Kaur / Bridget L Menasche / Jin Wei / Gabriel A Russell / John Huck / Jaewon Song / Aaron Ring / Akiko Iwasaki / Rohit K Jangra / Sanghyun Lee / David R Martinez / Walther Mothes / Pradeep D Uchil / John G Doench / Alicen B Spaulding / Ralph S Baric / Leonid Serebryannyy / Yaroslav Tsybovsky / Tongqing Zhou / Daniel C Douek / Craig B Wilen /
Abstract: Identifying receptors for bat coronaviruses is critical for spillover risk assessment, countermeasure development, and pandemic preparedness. While Middle East respiratory syndrome coronavirus (MERS- ...Identifying receptors for bat coronaviruses is critical for spillover risk assessment, countermeasure development, and pandemic preparedness. While Middle East respiratory syndrome coronavirus (MERS-CoV) uses DPP4 for entry, the receptors of many MERS-related betacoronaviruses remain unknown. The bat merbecovirus HKU5 was previously shown to have an entry restriction in human cells. Using both pseudotyped and full-length virus, we show that HKU5 uses Pipistrellus abramus bat ACE2 but not human ACE2 or DPP4 as a receptor. Cryo-electron microscopy analysis of the virus-receptor complex and structure-guided mutagenesis reveal a spike and ACE2 interaction that is distinct from other ACE2-using coronaviruses. MERS-CoV vaccine sera poorly neutralize HKU5 informing pan-merbecovirus vaccine design. Notably, HKU5 can also engage American mink and stoat ACE2, revealing mustelids as potential intermediate hosts. These findings highlight the versatility of merbecovirus receptor use and underscore the need for continued surveillance of bat and mustelid species.
History
DepositionJan 15, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48650.png

Downloads & links

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Map

FileDownload / File: emd_48650.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-1.1549621 - 1.8808463
Average (Standard dev.)-0.00007989818 (±0.035520297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48650_msk_1.map
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Additional map: #2

Fileemd_48650_additional_1.map
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Additional map: #1

Fileemd_48650_additional_2.map
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Half map: #2

Fileemd_48650_half_map_1.map
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Half map: #1

Fileemd_48650_half_map_2.map
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Sample components

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Entire : ACE2-ACT66266.1 in complex with HKU5-CTD (ABN10875)

EntireName: ACE2-ACT66266.1 in complex with HKU5-CTD (ABN10875)
Components
  • Complex: ACE2-ACT66266.1 in complex with HKU5-CTD (ABN10875)
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: ACE2-ACT66266.1 in complex with HKU5-CTD (ABN10875)

SupramoleculeName: ACE2-ACT66266.1 in complex with HKU5-CTD (ABN10875) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pipistrellus abramus bat coronavirus HKU5-related
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Pipistrellus abramus (Japanese house bat)
Molecular weightTheoretical: 92.874102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSSSWLLLS LVAVAGAQYT TEEEARRFLV KFNHEAENLS HESALASWDY NTNITDENAK KMNEADNKWS DFYKEQSKIA QGFPLQEIK DPIIKLQLQI LQQNGSSVLT AEKRKRLSTI LTTMSTIYST GKVCNPNNPQ QCFTLSGLED IMEKSKDYHE R LWVWEGWR ...String:
MSSSSWLLLS LVAVAGAQYT TEEEARRFLV KFNHEAENLS HESALASWDY NTNITDENAK KMNEADNKWS DFYKEQSKIA QGFPLQEIK DPIIKLQLQI LQQNGSSVLT AEKRKRLSTI LTTMSTIYST GKVCNPNNPQ QCFTLSGLED IMEKSKDYHE R LWVWEGWR SEVGKQLRPL YEEYVELKNE MARGNNYKDY GDYWRGDYET EGEKGYNYSR NYLMEDVDRI FLEIKPLYEQ LH AYVRAKL MKAYPSHISP TGCLPAHLLG DMWGRFWTNL YNLTVPLEKE PNIDVTDTMK KQSWDAEKIF KEAEKFYSSV GLP NMTPGF WRDSMLTEPS DGRQVVCHPT AWDLGKNDFR IKMCTKVTMD DFLTAHHEMG HIQYDMAYAN QSYLLRNGAN EGFH EAVGE VMSLSVATPK HLKGMGLLPS DFSENNETEI NFLLKQALTI VGTLPFTYML EKWRWMVFEG KIPKEQWMEK WWEMK REIV GVVEPLPHDE TYCDPASLFH VANDYSFIRY FTRTILEFQF QEALCRTAKH QGPLHKCDIS NSTEAGKKLN DMLKLG KST PWTYALEKIA ETKEMDAKPL LNYFNPLFRW LKEQNGNSVG WSVDSSPYSN QSIKVRISLK SALGEKAYEW NENEMYL FQ SSVAYAMRVY FLKAKNESIP FRAEDVRVSD EKKRVSFKFF VTSPTNMSDI IPRSEVEDAI RMSRSRINDA FRLDDNTL E FLGVQPTLGP PYQPPVTIWL IVFGVVMGVV VIGIGVLIFT GIRDRKKRNQ AENEENPYSS VNLSKGENNP GFQSGDDVQ TSF

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pipistrellus bat coronavirus HKU5
Molecular weightTheoretical: 149.814 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRSVLVLMC SLTFIGNLTR GQSVDMGHNG TGSCLDSQVQ PDYFESVHTT WPMPIDTSKA EGVIYPNGKS YSNITLTYTG LYPKANDLG KQYLFSDGHS APGRLNNLFV SNYSSQVESF DDGFVVRIGA AANKTGTTVI SQSTFKPIKK IYPAFLLGHS V GNYTPSNR ...String:
MIRSVLVLMC SLTFIGNLTR GQSVDMGHNG TGSCLDSQVQ PDYFESVHTT WPMPIDTSKA EGVIYPNGKS YSNITLTYTG LYPKANDLG KQYLFSDGHS APGRLNNLFV SNYSSQVESF DDGFVVRIGA AANKTGTTVI SQSTFKPIKK IYPAFLLGHS V GNYTPSNR TGRYLNHTLV ILPDGCGTIL HAFYCVLHPR TQQNCAGETN FKSLSLWDTP ASDCVSGSYN QEATLGAFKV YF DLINCTF RYNYTITEDE NAEWFGITQD TQGVHLYSSR KENVFRNNMF HFATLPVYQK ILYYTVIPRS IRSPFNDRKA WAA FYIYKL HPLTYLLNFD VEGYITKAVD CGYDDLAQLQ CSYESFEVET GVYSVSSFEA SPRGEFIEQA TTQECDFTPM LTGT PPPIY NFKRLVFTNC NYNLTKLLSL FQVSEFSCHQ VSPSSLATGC YSSLTVDYFA YSTDMSSYLQ PGSAGAIVQF NYKQD FSNP TCRVLATVPQ NLTTITKPSN YAYLTECYKT SAYGKNYLYN APGAYTPCLS LASRGFSTKY QSHSDGELTT TGYIYP VTG NLQMAFIISV QYGTDTNSVC PMQALRNDTS IEDKLDVCVE YSLHGITGRG VFHNCTSVGL RNQRFVYDTF DNLVGYH SD NGNYYCVRPC VSVPVSVIYD KASNSHATLF GSVACSHVTT MMSQFSRMTK TNLLARTTPG PLQTTVGCAM GFINSSMV V DECQLPLGQS LCAIPPTTSS RVRRATSGAS DVFQIATLNF TSPLTLAPIN STGFVVAVPT NFTFGVTQEF IETTIQKIT VDCKQYVCNG FKKCEDLLKE YGQFCSKINQ ALHGANLRQD ESIANLFSSI KTQNTQPLQA GLNGDFNLTM LQIPQVTTGE RKYRSTIED LLFNKVTIAD PGYMQGYDEC MQQGPQSARD LICAQYVAGY KVLPPLYDPY MEAAYTSSLL GSIAGASWTA G LSSFAAIP FAQSIFYRLN GVGITQQVLS ENQKIIANKF NQALGAMQTG FTTTNLAFNK VQDAVNANAM ALSKLAAELS NT FGAISSS ISDILARLDT VEQEAQIDRL INGRLTSLNA FVAQQLVRTE AAARSAQLAQ DKVNECVKSQ SKRNGFCGTG THI VSFAIN APNGLYFFHV GYQPTSHVNA TAAYGLCNTE NPQKCIAPID GYFVLNQTTS TVADSDQQWY YTGSSFFHPE PITE ANSKY VSMDVKFENL TNRLPPPLLS NSTDLDFKEE LEEFFKNVSS QGPNFQEISK INTTLLNLNT ELMVLSEVVK QLNES YIDL KELGNYTFYQ KWPWYIWLGF IAGLVALALC VFFILCCTGC GTSCLGKLKC NRCCDSYDEY EVEKIHVH

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: 8 / 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

Concentration3.7 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 10702 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2125866
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 242675
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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