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- EMDB-60483: Cryo-EM structure of P.nat ACE2 mutant in complex with MOW15-22 RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-60483
TitleCryo-EM structure of P.nat ACE2 mutant in complex with MOW15-22 RBD
Map data
Sample
  • Complex: P.nat ACE2-MOW15-22 RBD
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: MOW15-22 RBD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsACE2 / RBD / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Biological speciesPipistrellus nathusii (Nathusius's pipistrelle) / Middle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsTang J / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2025
Title: Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses.
Authors: Cheng-Bao Ma / Chen Liu / Young-Jun Park / Jingjing Tang / Jing Chen / Qing Xiong / Jimin Lee / Cameron Stewart / Daniel Asarnow / Jack Brown / M Alejandra Tortorici / Xiao Yang / Ye-Hui Sun ...Authors: Cheng-Bao Ma / Chen Liu / Young-Jun Park / Jingjing Tang / Jing Chen / Qing Xiong / Jimin Lee / Cameron Stewart / Daniel Asarnow / Jack Brown / M Alejandra Tortorici / Xiao Yang / Ye-Hui Sun / Yuan-Mei Chen / Xiao Yu / Jun-Yu Si / Peng Liu / Fei Tong / Mei-Ling Huang / Jing Li / Zheng-Li Shi / Zengqin Deng / David Veesler / Huan Yan /
Abstract: The angiotensin-converting enzyme 2 (ACE2) receptor is shared by various coronaviruses with distinct receptor-binding domain (RBD) architectures, yet our understanding of these convergent acquisition ...The angiotensin-converting enzyme 2 (ACE2) receptor is shared by various coronaviruses with distinct receptor-binding domain (RBD) architectures, yet our understanding of these convergent acquisition events remains elusive. Here, we report that two bat MERS-related coronaviruses (MERSr-CoVs) infecting Pipistrellus nathusii (P.nat)-MOW15-22 and PnNL2018B-use ACE2 as their receptor, with narrow ortholog specificity. Cryoelectron microscopy structures of the MOW15-22/PnNL2018B RBD-ACE2 complexes unveil an unexpected and entirely distinct binding mode, mapping >45 Å away from that of any other known ACE2-using coronaviruses. Functional profiling of ACE2 orthologs from 105 mammalian species led to the identification of host tropism determinants, including an ACE2 N432-glycosylation restricting viral recognition, and the design of a soluble P.nat ACE2 mutant with potent viral neutralizing activity. Our findings reveal convergent acquisition of ACE2 usage for merbecoviruses found in European bats, underscoring the extraordinary diversity of ACE2 recognition modes among coronaviruses and the promiscuity of this receptor.
History
DepositionJun 9, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60483.png

Downloads & links

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Map

FileDownload / File: emd_60483.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 200 pix.
= 190. Å		0.95 Å/pix.
x 200 pix.
= 190. Å		0.95 Å/pix.
x 200 pix.
= 190. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.9875267 - 2.2903867
Average (Standard dev.)0.0011234555 (±0.06262494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 190.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60483_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: #1

Fileemd_60483_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : P.nat ACE2-MOW15-22 RBD

EntireName: P.nat ACE2-MOW15-22 RBD
Components
  • Complex: P.nat ACE2-MOW15-22 RBD
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: MOW15-22 RBD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: P.nat ACE2-MOW15-22 RBD

SupramoleculeName: P.nat ACE2-MOW15-22 RBD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pipistrellus nathusii (Nathusius's pipistrelle)

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pipistrellus nathusii (Nathusius's pipistrelle)
Molecular weightTheoretical: 90.767672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EEKAREFLDK FNSEAENWSH ESALASWDYN TNINDKNAQK MNEADSKWSA FYKEHSKLAQ GFPLQEIQNS TIKLQLQILQ QNGSSVLTA EKSKRLSTIL TTMSTIYSTG KVCNPNNPQQ CFTLSGLEDI MEKSKDYHQR LWIWEGWRSE VGKQLRPLYE E YVALKNEM ...String:
EEKAREFLDK FNSEAENWSH ESALASWDYN TNINDKNAQK MNEADSKWSA FYKEHSKLAQ GFPLQEIQNS TIKLQLQILQ QNGSSVLTA EKSKRLSTIL TTMSTIYSTG KVCNPNNPQQ CFTLSGLEDI MEKSKDYHQR LWIWEGWRSE VGKQLRPLYE E YVALKNEM ARGNNYKDYG DYWRGDYETE GGDGYNYSRN HLIEDVDRIF LEIKPLYEQL HAYVRAKLMN AYPSRISPTG CL PAHLLGD MWGRFWTNLY NLTVPFEKKQ NIDVTDTMKK QSWDAEKIFK EAEKFYLSVG LHNMTPEFWN NSMLTEPSDG RQV VCHPTA WDLGKNDFRI KMCTKVTMDD FLTAHHEMGH IQYDMAYAKQ PYLLRNGANE GFHEAVGEIM SLSAATPKHL KDLG LLAQN YPEDYETEIN FLLKQALNIV GTLPFTYMLE KWRWMVFEGK IPKEQWMEKW WEMKREIVGV VEPLPHDETY CDPAS LFHV ANDYSFIRYF TRTILEFQFQ EALCQIANHT GPLHKCDISN STEAGKQLKN MLELGKSKPW TFALEQIART KEMDAK PLL NYFKPLFSWL KELNGNSVGW SADWSPYSEQ SIKVRISLKS ALGEKAYEWN DNEMYLFRSS VAYAMRVYFL KVKNETI PF RAEDVWVSDE KIRVSFKFFV TSPTNVSDII PRSEVEDAIR MSRGRINDAF RLDDKTLEFL GIQPTLGPPY QPPVTIWL I VFGVVMGMVV IGIGVLIFTG IRDRKKKNQA ENEENPYSSV NLSKGENNPG FQSGDDVQTS F

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Macromolecule #2: MOW15-22 RBD

MacromoleculeName: MOW15-22 RBD / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 23.646434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ECDFTKLFIG QVPQPYEFGR LVFTNCNYNF TKLLSYFQVN TFQCQKVTPE SIATGCYSSL TVDWFAYRVE DKSDLLPGSS SDLQRFNYK PTYSNPTCLI SAYTNLVPLG GVNPTNYTTL TNCYGCVDKD PANPWGDQIC IPEFVTEVEP GFRPKPSCAR V GLEGHISG ...String:
ECDFTKLFIG QVPQPYEFGR LVFTNCNYNF TKLLSYFQVN TFQCQKVTPE SIATGCYSSL TVDWFAYRVE DKSDLLPGSS SDLQRFNYK PTYSNPTCLI SAYTNLVPLG GVNPTNYTTL TNCYGCVDKD PANPWGDQIC IPEFVTEVEP GFRPKPSCAR V GLEGHISG NDTYSAIVTN GELDSTGDPI WRKGVALTKQ PIDSSRADLA FFVSV

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

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

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / 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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 244733
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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