[English] 日本語
Yorodumi
- EMDB-61602: Cryo-EM structure of HKU25-BatCoV S-trimer stabilized with 2P and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61602
TitleCryo-EM structure of HKU25-BatCoV S-trimer stabilized with 2P and x1 disulfide bond
Map data
Sample
  • Organelle or cellular component: HKU25-BatCoV Spike protein (with 2P-x1 stabilization)
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: LINOLEIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsspike protein / VIRAL PROTEIN
Function / homology
Function and homology information


virion component / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 / membrane
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 / Fibritin C-terminal / Fibritin C-terminal region / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Fibritin C-terminal / Fibritin C-terminal region / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesHypsugo bat coronavirus HKU25 / Tequatrovirus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsYuan H / Xiong X
Funding support3 items
OrganizationGrant numberCountry
Other governmentSRPG22-002
Other government2021YFA1300903
Other government2022A1515110495
CitationJournal: Sci Adv / Year: 2025
Title: Structures and receptor binding activities of merbecovirus spike proteins reveal key signatures for human DPP4 adaptation.
Authors: Hang Yuan / Jingjing Wang / Yong Ma / Zimu Li / Xijie Gao / Gul Habib / Banghui Liu / Jing Chen / Jun He / Peng Zhou / Zheng-Li Shi / Xinwen Chen / Xiaoli Xiong /
Abstract: Merbecoviruses from bats, pangolins, and hedgehogs pose significant zoonotic threats, with a limited understanding of receptor binding by their spike (S) proteins. Here, we report cryo-EM structures ...Merbecoviruses from bats, pangolins, and hedgehogs pose significant zoonotic threats, with a limited understanding of receptor binding by their spike (S) proteins. Here, we report cryo-EM structures of GD-BatCoV (BtCoV-422) and SE-PangolinCoV (MjHKU4r-CoV-1) RBDs in complex with human DPP4 (hDPP4). These structures exhibit a substantial offset in their hDPP4 interaction interfaces, revealing a conserved hydrophobic cluster as a convergent signature of DPP4 binding within the MERS-HKU4 clade of merbecoviruses. Structure-guided mutagenesis demonstrates that favorable interactions are distributed across multiple receptor binding motif (RBM) regions, working synergistically to confer high-affinity hDPP4 binding. Swapping of the merbecovirus RBM regions indicate limited plasticity and interchangeability among these regions. In addition, we report cryo-EM structures of six merbecovirus S-trimers. Structure-based phylogenetics suggests that hDPP4-binding merbecoviruses undergo convergent evolution, while ACE2-binding merbecoviruses exhibit diversification in their binding mechanisms. These findings offer critical insights into merbecovirus receptor utilization, providing a structural understanding for future surveillance.
History
DepositionSep 20, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61602.png

Downloads & links

-
Map

FileDownload / File: emd_61602.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.779
Minimum - Maximum-4.3090844 - 7.1666203
Average (Standard dev.)-0.0003975084 (±0.23766358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61602_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61602_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HKU25-BatCoV Spike protein (with 2P-x1 stabilization)

EntireName: HKU25-BatCoV Spike protein (with 2P-x1 stabilization)
Components
  • Organelle or cellular component: HKU25-BatCoV Spike protein (with 2P-x1 stabilization)
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: LINOLEIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: HKU25-BatCoV Spike protein (with 2P-x1 stabilization)

SupramoleculeName: HKU25-BatCoV Spike protein (with 2P-x1 stabilization) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Hypsugo bat coronavirus HKU25

-
Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 151.971281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTLSMFLLMF LLTHIKGDVD LGPDSSAQSC QEVDIQPQYF QKDWTKPIDP AKADGIIYPT GRSYSNITLS YQGLFPRQGD QGQLYLYSV SHADPNTGKM GPDGIGKLFI SNYTNETNTF DNGFVVRIGD AANSSYPIII SPQGPARTIK KIYPAFMLGA Y IGNFTNNR ...String:
MTLSMFLLMF LLTHIKGDVD LGPDSSAQSC QEVDIQPQYF QKDWTKPIDP AKADGIIYPT GRSYSNITLS YQGLFPRQGD QGQLYLYSV SHADPNTGKM GPDGIGKLFI SNYTNETNTF DNGFVVRIGD AANSSYPIII SPQGPARTIK KIYPAFMLGA Y IGNFTNNR TVRYLNHTLV ILPEGCGTSL SVFYCVLIPR TQHRCPEDNA YSSYVIWETP HQDCEGSTVN RNISLNAFKH YF NLTQCKF FYSYNITEDE HAEWFGITQD ARGVHLYSSR KGDLYGGNMF LFASLPIYDT LKYYTVIPRS IRSKYNSRQG WAA FYIYKL HQLTYLLDFT VDGYIRRAVD CGHDDLAQLR CSYESFDVDS GVYSVSSFEA QPRGAFIEQS SGKECDFSPM LTGT PPQVY NFRRLVFTDC NYNLTKLLSL FQVSEFSCHQ VCPDALASGC YSSLTVDYFA YPTSLASYLQ QGSTGEITQY NYKQD FSNP TCRILATAPA NITLTKPSNY NWLTQCYKGS AFGNQPHYVQ TGQYTPCLGL AVQGFSAAYQ SHRDPITKLV ATGNIA AMT DNLQMAFIIS VQYGTDTNSV CPMQALRNDT SVHDKLGQCI DYSLYGLTGR GVFQNCTAVG LSQQRFVYDG FDILTGY HS DDGNYYCVRP CVSVPLSVVY DKPSNNYATI FGSVACDYVN TMTTQLSRMT QAKLRSRSFT TPIQTAVGCV IGLVNSSL V VDDDKCTLPL GQSLCAVPSK NRDTTSNLQL AVINFTRPHL VEALNSSGFV VQIPTNFSFS ITQEYIQTTI QKVTVDCKQ YVCNGFEKCE TLLREYGQFC AKINQALHGA NLRQDESVAN LFANIKTQTT QALDAGLNGD FNLTLLQVPK VTTSQYSYRS TIEDLLFNK VTIADPGYMQ GYDECMQQGP PSARDLICAQ FVAGYKVLPP LYDPNMEAAY TSSLLGSILG AGWTAGLSSF A AIPFAQSI FYRMNGIGIT QQVLSENQKQ IDKKFNQALN AMQTGFTTTN LAFSKVQDAV NANAQALAKL ASELSNTFGA IS SSISDIL KRLCPPEQEA QIDRLINGRL TSLNAFVAQQ LVRSETAARS AQLASDKVNE CVKSQSKRNG FCGSGTHIVS FVI NAPDGL YFFHVGYVPT DHINATAAYG LCNNDNPPRC IAPIDGYFVR NSSTTRDAND EWYYTGSSYY NPEPISMANT RYVS QDTKF ENLTTNIPPP LLNRTDSDFK DELEEFFKNV SSQGPNFAEI SKINTTLLDL STEMNALNEV VKQLNQSYID LKELG NYSY YQKWPGSGYI PEAPRDGQAY VRKDGEWVLL STFLLEVLFQ GPGHHHHHHH HSAWSHPQFE KGGGSGGGGS GGSAWS HPQ FEKSA

UniProtKB: Spike glycoprotein, Fibritin

-
Macromolecule #4: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 4 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 38 / 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: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6q04

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110266
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