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- EMDB-46512: Structure of the HKU5 RBD bound to the P. abramus ACE2 receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-46512
TitleStructure of the HKU5 RBD bound to the P. abramus ACE2 receptor
Map data
Sample
  • Complex: HKU5 RBD bound to the P. abramus ACE2 receptor
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsMERS-related HKU5 coronaviruses / MERSr-CoV / Spike glycoprotein / fusion protein / Pipistrellus abramus ACE2 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / inhibitor / 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 speciesHomo sapiens (human) / Pipistrellus abramus (Japanese house bat) / Pipistrellus bat coronavirus HKU5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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)AI158186 United States
CitationJournal: Cell / Year: 2025
Title: Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses.
Authors: Young-Jun Park / Chen Liu / Jimin Lee / Jack T Brown / Cheng-Bao Ma / Peng Liu / Risako Gen / Qing Xiong / Samantha K Zepeda / Cameron Stewart / Amin Addetia / Caroline J Craig / M Alejandra ...Authors: Young-Jun Park / Chen Liu / Jimin Lee / Jack T Brown / Cheng-Bao Ma / Peng Liu / Risako Gen / Qing Xiong / Samantha K Zepeda / Cameron Stewart / Amin Addetia / Caroline J Craig / M Alejandra Tortorici / Abeer N Alshukairi / Tyler N Starr / Huan Yan / David Veesler /
Abstract: DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity of ACE2 utilization among ...DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity of ACE2 utilization among merbecoviruses and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. We defined the molecular determinants of receptor species tropism and identified a single amino acid mutation enabling HKU5 to utilize human ACE2, providing proof of principle for machine-learning-assisted outbreak preparedness. We show that MERS-CoV and HKU5 have markedly distinct antigenicity and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution, as several merbecovirus clades independently evolved ACE2 utilization, and pave the way for developing countermeasures against viruses poised for human emergence.
History
DepositionAug 9, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46512.png

Downloads & links

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Map

FileDownload / File: emd_46512.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. Å		1 Å/pix.
x 320 pix.
= 320. Å		1 Å/pix.
x 320 pix.
= 320. 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: 0.65
Minimum - Maximum-3.8521745 - 4.9299083
Average (Standard dev.)0.00033037693 (±0.06345048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_46512_additional_1.map
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Half map: #2

Fileemd_46512_half_map_1.map
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Half map: #1

Fileemd_46512_half_map_2.map
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Sample components

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Entire : HKU5 RBD bound to the P. abramus ACE2 receptor

EntireName: HKU5 RBD bound to the P. abramus ACE2 receptor
Components
  • Complex: HKU5 RBD bound to the P. abramus ACE2 receptor
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: HKU5 RBD bound to the P. abramus ACE2 receptor

SupramoleculeName: HKU5 RBD bound to the P. abramus ACE2 receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1
Details: residues (-6)-16 expression signal peptide; residues 725-730 thrombin cleavage site; residues 731-750 expression AVI tag; residues 751-753 expression linker; residues 754-761 expression HIS tag
Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Pipistrellus abramus (Japanese house bat)
Molecular weightTheoretical: 89.172906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAQYTTEE EARRFLVKFN HEAENLSHES ALASWDYNTN ITDENAKKMN EADNKWSDFY KEQSKIAQG FPLQEIKDPI IKLQLQILQQ NGSSVLTAEK RKRLSTILTT MSTIYSTGKV CNPNNPQQCF TLSGLEDIME K SKDYHERL ...String:
MPMGSLQPLA TLYLLGMLVA SVLAQYTTEE EARRFLVKFN HEAENLSHES ALASWDYNTN ITDENAKKMN EADNKWSDFY KEQSKIAQG FPLQEIKDPI IKLQLQILQQ NGSSVLTAEK RKRLSTILTT MSTIYSTGKV CNPNNPQQCF TLSGLEDIME K SKDYHERL WVWEGWRSEV GKQLRPLYEE YVELKNEMAR GNNYKDYGDY WRGDYETEGE KGYNYSRNYL MEDVDRIFLE IK PLYEQLH AYVRAKLMKA YPSHISPTGC LPAHLLGDMW GRFWTNLYNL TVPLEKEPNI DVTDTMKKQS WDAEKIFKEA EKF YSSVGL PNMTPGFWRD SMLTEPSDGR QVVCHPTAWD LGKNDFRIKM CTKVTMDDFL TAHHEMGHIQ YDMAYANQSY LLRN GANEG FHEAVGEVMS LSVATPKHLK GMGLLPSDFS ENNETEINFL LKQALTIVGT LPFTYMLEKW RWMVFEGKIP KEQWM EKWW EMKREIVGVV EPLPHDETYC DPASLFHVAN DYSFIRYFTR TILEFQFQEA LCRTAKHQGP LHKCDISNST EAGKKL NDM LKLGKSTPWT YALEKIAETK EMDAKPLLNY FNPLFRWLKE QNGNSVGWSV DSSPYSNQSI KVRISLKSAL GEKAYEW NE NEMYLFQSSV AYAMRVYFLK AKNESIPFRA EDVRVSDEKK RVSFKFFVTS PTNMSDIIPR SEVEDAIRMS RSRINDAF R LDDNTLEFLG LVPRGSSSGG SGLNDIFEAQ KIEWHEGGSH HHHHHHH

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2
Details: residues 358-388 expression signal peptide; residues 588-593 thrombin cleavage site; residues 594-598 expression linker; residues 599-613 expression AVI tag; residues 614-616 expression ...Details: residues 358-388 expression signal peptide; residues 588-593 thrombin cleavage site; residues 594-598 expression linker; residues 599-613 expression AVI tag; residues 614-616 expression linker; residues 617-624 expression HIS tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pipistrellus bat coronavirus HKU5
Molecular weightTheoretical: 29.22484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQECDFTPM LTGTPPPIYN FKRLVFTNCN YNLTKLLSLF QVSEFSCHQV SPSSLATGC YSSLTVDYFA YSTDMSSYLQ PGSAGEIVQF NYKQDFSNPT CRVLATVPQN LTTITKPSNY AYLTECYKTS A YGKNYLYN ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQECDFTPM LTGTPPPIYN FKRLVFTNCN YNLTKLLSLF QVSEFSCHQV SPSSLATGC YSSLTVDYFA YSTDMSSYLQ PGSAGEIVQF NYKQDFSNPT CRVLATVPQN LTTITKPSNY AYLTECYKTS A YGKNYLYN APGGYTPCLS LASRGFSTKY QSHSDGELTT TGYIYPVTGN LQMAFIISVQ YGTDTNSVCP MQLVPRGSSS GG SGLNDIF EAQKIEWHEG GSHHHHHHHH

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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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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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

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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 550684
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Image processing #2

Image processing ID2
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 550684
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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