[English] 日本語
Yorodumi
- EMDB-45253: Merbecovirus MOW15-22 Spike glycoprotein RBD bound to the P. davy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45253
TitleMerbecovirus MOW15-22 Spike glycoprotein RBD bound to the P. davyi ACE2
Map data
Sample
  • Complex: MOW15-22 RBD bound to the P. davyi ACE2 ectodomain
    • Protein or peptide: MOW15-22 RBD
    • Protein or peptide: Pteronotus davyi ACE2 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMerbecovirus / MERS-related coronaviruses / MOW15-22 Spike glycoprotein / fusion protein / P. davyi ACE2 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN
Biological speciesSarbecovirus / Merbecovirus / Pteronotus davyi (Davy's naked-backed bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 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)AI158186 United States
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 7, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45253.png

Downloads & links

-
Map

FileDownload / File: emd_45253.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. Å		1 Å/pix.
x 320 pix.
= 320. Å		1 Å/pix.
x 320 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.2693305 - 6.0532646
Average (Standard dev.)0.00033461358 (±0.06883713)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: #1

Fileemd_45253_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_45253_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_45253_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MOW15-22 RBD bound to the P. davyi ACE2 ectodomain

EntireName: MOW15-22 RBD bound to the P. davyi ACE2 ectodomain
Components
  • Complex: MOW15-22 RBD bound to the P. davyi ACE2 ectodomain
    • Protein or peptide: MOW15-22 RBD
    • Protein or peptide: Pteronotus davyi ACE2 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: MOW15-22 RBD bound to the P. davyi ACE2 ectodomain

SupramoleculeName: MOW15-22 RBD bound to the P. davyi ACE2 ectodomain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sarbecovirus

-
Macromolecule #1: MOW15-22 RBD

MacromoleculeName: MOW15-22 RBD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Merbecovirus
Molecular weightTheoretical: 34.898027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTYSVSSFEA KPQGSFIESV YEGNECDFTK LFIGQVPQPY EFGRLVFTNC NYNFTKLLS YFQVNTFQCQ KVTPESIATG CYSSLTVDWF AYRVEDKSDL LPGSSSDLQR FNYKPTYSNP TCLISAYTNL V PLGGVNPT ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTYSVSSFEA KPQGSFIESV YEGNECDFTK LFIGQVPQPY EFGRLVFTNC NYNFTKLLS YFQVNTFQCQ KVTPESIATG CYSSLTVDWF AYRVEDKSDL LPGSSSDLQR FNYKPTYSNP TCLISAYTNL V PLGGVNPT NYTTLTNCYG CVDKDPANPW GDQICIPEFV TEVEPGFRPK PSCARVGLEG HISGNDTYSA IVTNGELDST GD PIWRKGV ALTKQPIDSS RADLAFFVSV QIDAQSSSVC PLGAPKLVPR GSSSGGSGLN DIFEAQKIEW HEGGSHHHHH HHH

-
Macromolecule #2: Pteronotus davyi ACE2 ectodomain

MacromoleculeName: Pteronotus davyi ACE2 ectodomain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pteronotus davyi (Davy's naked-backed bat)
Molecular weightTheoretical: 89.589047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAQILTED EKAKEFLEKF DLEAEKLYHQ SSLASWNYNT NITEENVKKM NEADREWSTF YENMTKIAK NYNLSQITDD KVKRQLQALQ QNGLSEDENK RLNNILNEMS TIYSTGKVCK PNNPQQCLLL ATGLEDIMQY S KDYDERLW ...String:
MPMGSLQPLA TLYLLGMLVA SVLAQILTED EKAKEFLEKF DLEAEKLYHQ SSLASWNYNT NITEENVKKM NEADREWSTF YENMTKIAK NYNLSQITDD KVKRQLQALQ QNGLSEDENK RLNNILNEMS TIYSTGKVCK PNNPQQCLLL ATGLEDIMQY S KDYDERLW AWEGWRSQVG KQLRPLYEKY VDLKNEMARE KNYEDYGDYW RGDYETDGKE DYAYSRNQLI DDVERTFEEI KP LYEHLHA YVRTKLMDAY PSRISPTGCL PAHLLGDMWG RFWTNLYDLT VPYGEKPTID VTAAMINQSW DAEKIFKEAE KFF MSVGLF NMTQGFWNNS MLTKPDDGRE VVCHPTAWDL GNNDFRIKMC TKVTMDDFLT AHHEMGHIQY DMAYAKQPFL LRNG ANEGF HEAVGEIMSL SAATPKHLKD LGLLAQNYPE DYETEINFLL KQALNIVGTL PFTYMLEKWR WMVFKGQIPK DQWTK KWWE MKRDIVGVVE PVPHDETYCD AASLFHVAND YSFIRYYTRT IFQFQFQEAL CRTAQHTGPL HKCDISNSTA AGEKLL KML ELGKSQPWTF ALENIVGERK INVRPLLDYF RPLFNWLKEQ NSNSFVGWRT DWSPYVDQSI KVRISLKSAL GDKAYEW ND NEMYFFQSSV AYAMRVYFSN FKNQTTPFGV ENVQVRNLKP RVSFNFFVTS PKNVSDIIPR SEVVEAIRMS RGRINDAF R LDDNSLEFLG LVPRGSSSGG SGLNDIFEAQ KIEWHEGGSH HHHHHHH

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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: 3.5 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 705956
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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://pdbjlvh1.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