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- EMDB-61600: Cryo-EM structure of SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) S-trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-61600
TitleCryo-EM structure of SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) S-trimer
Map data
Sample
  • Organelle or cellular component: SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) Spike protein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
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
Fibritin / Spike glycoprotein
Similarity search - Component
Biological speciesCoronavirus Neoromicia/PML-PHE1/RSA/2011 / Enterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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

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Structure visualization

Supplemental images

emd_61600.png

Downloads & links

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Map

FileDownload / File: emd_61600.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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.12670606 - 0.2500368
Average (Standard dev.)0.00008072749 (±0.007916003)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_61600_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61600_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 : SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) Spike protein

EntireName: SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) Spike protein
Components
  • Organelle or cellular component: SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) Spike protein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID

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Supramolecule #1: SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) Spike protein

SupramoleculeName: SA-BatCoV (Neoromicia/PML-PHE1/RSA/2011) Spike protein
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Coronavirus Neoromicia/PML-PHE1/RSA/2011
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 150.804984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTYSVFPLMC LLTFIGANAK IVTLPGNDAT GYCPSVDMQP SYFIQHNWPE PIDMNKADGV IYPNGRTYSN ITLQTTNLFP KNGDLGTQY VYSASNHKST ANDAFISNYS YYGNPFGDGI VIRIGQNANK TGSVIVGQAQ TTMKKIYPAL MLGSSFGNFS A NNKSGAYF ...String:
MTYSVFPLMC LLTFIGANAK IVTLPGNDAT GYCPSVDMQP SYFIQHNWPE PIDMNKADGV IYPNGRTYSN ITLQTTNLFP KNGDLGTQY VYSASNHKST ANDAFISNYS YYGNPFGDGI VIRIGQNANK TGSVIVGQAQ TTMKKIYPAL MLGSSFGNFS A NNKSGAYF NHTLLILPSK CGTVFQVAYC LLQPRTESKC PGNSNYVSYF LADSPSDCSS TSDEIRRNGL RDIRKFFNLV NC TYFEEFN VTADERAEWF GIVQDAQGVH LYTSRKNGFN SNNLFLFATV PIYDKLNYYT VIPRSVITPS NQRDAWAAFY IYP LHQLSY LLNFDVNGYI TQAADCGYND YTQLICSYGD FNMKSGVYST SYYSAKPVGA YYEAHVYPDC NFTELFRERA PTIM QYKRE VFTRCNYNLS LLLSLVQVDE FVCDKITPEA LATGCYSSLT VDWFAFPYAW KSYLAIGSAD RIVRFNYNQD YSNPS CRIH SKVNSSIGIS YAGAYSYITN CNYGATNKDD VVKPGGRASQ QCITGALNSP TTGQLWAYNF GGVPYRVSRL TYTDHL SDP LDMVYVITVK YEPGAETVCP KQIRPDYSTN ITHLLGSCIS YDIYGITGTG VFQLCNATGI RQQKFVYDKF DNIIGFH SD DGNYYCVAPC VSVPVSVIYD DKTNQYATLF GSVACQHIST MAAQFSRETR ASLVSRNMQN LLQTSVGCVM GFHETNDT V EECHLSLGQS LCAIPPNTNL RSGRSTFGLG SLAYNSPLRV DALNSSEFKV SLPLNFTFGV TQEYIETSIQ KITVDCKQY VCNGFAKCEK LLEQYGQFCS KINQALHGAN LRQDDSVRNL FESVKTPQTV PLTTGFGGEF NLTLLEPLSV STGSSNARSA LEELLFDSV TIADPGYMQG YDDCMQQGPA SARDLICAQY VAGYKVLPPL MDVNMEAAYT SSLLGSIAGA GWTAGLSSFA A IPFAQSIF YRLNGVGITQ QVLSENQKII ANKFNQALGA MQTGFTTTNE AFQKVQDAVN TNAQALAKLA SELSNTFGAI SS SIGDIIQ RLDVLEQEVQ IDRLINGRLT TLNAFVAQQL VRSESAARSA QLAKDKVNEC VKSQSTRSGF CGQGTHIVSF VIN APNGLY FMHVGYHPSQ HIEVVAAYGL CDSANPTNCI APVNGYFIKN QTTRSADEWS YTGSSFYAPE PITTLNTRYV APQV TFQNI SNNLPPPLLS NSTGTDFKDE LDEFFKNVST NIPNFGALTQ INTTLLDLSG EMLALQEVVK ALNESYIDLK ELGNY TYYN KWPGSGYIPE APRDGQAYVR KDGEWVLLST FLLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSHP QFE KSA

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 33 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

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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: 7.4
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196103
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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