[English] 日本語
Yorodumi
- EMDB-49093: Eptesicus fuscus ACE2 peptidase domain bound to VsCoV-a7 RBD complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49093
TitleEptesicus fuscus ACE2 peptidase domain bound to VsCoV-a7 RBD complex
Map data
Sample
  • Complex: ACE2 peptidase domain bound to VsCoV-a7 RBD complex
    • Protein or peptide: Angiotensin-converting enzyme 2
    • Protein or peptide: VsCoV-a7-S RBD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water
KeywordsVirus / HKU25 clade MERS-related coronaviruses / ACE2 / Glycoprotein / Receptor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / HYDROLASE-VIRAL PROTEIN complex
Biological speciesMerbecovirus / Eptesicus fuscus (big brown bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsPark YJ / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
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

-
Structure visualization

Supplemental images

emd_49093.png

Downloads & links

-
Map

FileDownload / File: emd_49093.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0011 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-3.0689044 - 4.741046
Average (Standard dev.)0.00017871315 (±0.08017742)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: #1

Fileemd_49093_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_49093_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49093_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ACE2 peptidase domain bound to VsCoV-a7 RBD complex

EntireName: ACE2 peptidase domain bound to VsCoV-a7 RBD complex
Components
  • Complex: ACE2 peptidase domain bound to VsCoV-a7 RBD complex
    • Protein or peptide: Angiotensin-converting enzyme 2
    • Protein or peptide: VsCoV-a7-S RBD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water

-
Supramolecule #1: ACE2 peptidase domain bound to VsCoV-a7 RBD complex

SupramoleculeName: ACE2 peptidase domain bound to VsCoV-a7 RBD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Merbecovirus / Strain: VsCoV-a7

-
Macromolecule #1: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Details: GenBank XM_008154928.2 / Number of copies: 1 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2
Source (natural)Organism: Eptesicus fuscus (big brown bat)
Molecular weightTheoretical: 89.451859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGSSWLFLS LVAVTAAQST TEKNATIFLE NFNSEAEDLS HESALASWNY NTNITDENAQ KMNEADSKWS AFYEKQSKLA QTYPLQEIQ NLTIKLQLQV LQQNGSSVLT ADKSKRLSTI LTTMSTIYST GKVCNPNNPQ ECLTLSGLED IMEKSKDYNQ R LWVWEGWR ...String:
MSGSSWLFLS LVAVTAAQST TEKNATIFLE NFNSEAEDLS HESALASWNY NTNITDENAQ KMNEADSKWS AFYEKQSKLA QTYPLQEIQ NLTIKLQLQV LQQNGSSVLT ADKSKRLSTI LTTMSTIYST GKVCNPNNPQ ECLTLSGLED IMEKSKDYNQ R LWVWEGWR SEVGKQLRPL YEEYVVLKNE MARGNNYEDY GDYWRGDYET EGENGYNYSR SQLTEDVDRI FLEIKPLYEH LH AYVRAKL MDTYPSRISP TGCLPAHLLG DMWGRFWTNL YNLTVPFEQK PNIDVTDAMK EQSWDAEKIF KEAEKFYMSV GLP SMTPGF WNNSMLTEPG DGRKVVCHPT AWDLGKNDFR IKMCTKVTMD DFLTAHHEMG HIQYDMAYAT QPYLLRNGAN EGFH EAVGE VMSLSVATPK HLKGMGLLPS DFSEDNETEI NFLLKQALNI VGTLPFTYML EKWRWMVFKG EIPKEQWMKK WWEMK REIV GVVEPLPHDE TYCDPASLFH VANDYSFIRY FTRTIFEFQF QEALCQIAKH QGPLHKCDIS NSTEAGNKLL EMLKLG KSK PWTFALEKIT GTKKMDAKPL LNYFEPLFTW LKEQNGNSVG WHSGNYVGWS SDWSPYADQS IKVRISLKSA LGEKAYE WN DNEMYLFRSS VAYAMREYFL KVKNQTIPFR AEDVWVNDVK PRVSFKFFVT SPTNMSDIIP RSEVEDAIRM SRSRINAA F RLDDNSLEFL GIQPTLGPPY QPPVTIGLND IFEAQKIEWH EGGSHHHHHH HH

-
Macromolecule #2: VsCoV-a7-S RBD

MacromoleculeName: VsCoV-a7-S RBD / type: protein_or_peptide / ID: 2 / Details: GenBank BDI08829.1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Merbecovirus / Strain: VsCoV-a7
Molecular weightTheoretical: 29.494377 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTECDFTSML TAVPPQVYNF SRLVFTNCNY NLTKLLSLFQ VTEFSCHQVS PDALASGCY SSLTVDYFAY PSYLASYLHP GSTGEIAQYN YKQDFSNPTC RILATVPANL TIPKPARYMW LTQCYSYSAF G NTPLYVKP ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTECDFTSML TAVPPQVYNF SRLVFTNCNY NLTKLLSLFQ VTEFSCHQVS PDALASGCY SSLTVDYFAY PSYLASYLHP GSTGEIAQYN YKQDFSNPTC RILATVPANL TIPKPARYMW LTQCYSYSAF G NTPLYVKP SQYTPCLSLA SQGFDADSQT HRDTVNKMAA TGRIAAMSGN LQMAFVISVQ YGTDANSVCP MQAVRLVPRG SS SGGSGLN DIFEAQKIEW HEGGSHHHHH HHH

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #5: ZINC ION

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

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 163 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 578871
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more