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- EMDB-60253: Cryo-EM structure of the spike glycoprotein from Bat SARS-like co... -

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Basic information

Entry
Database: EMDB / ID: EMD-60253
TitleCryo-EM structure of the spike glycoprotein from Bat SARS-like coronavirus (Bat SL-CoV) WIV1 in locked state
Map data
Sample
  • Complex: Bat SARS-like coronavirus (SL-CoV) WIV1 spike (S) glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: LINOLEIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsBat SARS-like coronavirus / WIV1 / spike glycoprotein / viral protein
Function / homology
Function and homology information


positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 ...positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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
Biological speciesBat SARS-like coronavirus WIV1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsLiu C / Beck F / Nagy I / Bohn S / Plitzko J / Baumeister W / Zhang X / Zinzula L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Cryo-EM structure of locked spike glycoprotein from bat SARS-like coronavirus WIV1, molecular dynamics and biophysics across host range.
Authors: Chuan Liu / Jingjing Zheng / Yuhan Wang / Florian Beck / István Nagy / Stefan Bohn / Jürgen M Plitzko / Wolfgang Baumeister / Xiaoxiao Zhang / Liping Sun / Luca Zinzula /
Abstract: As made evident by severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 pandemics, the possibility of a SARS-like coronavirus (SL-CoV) emerging again in humankind after ...As made evident by severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 pandemics, the possibility of a SARS-like coronavirus (SL-CoV) emerging again in humankind after zoonotic spillover represents a significant global health threat. Given the role of spike (S) glycoprotein in mediating SL-CoV cell entry and cross-species transmission, there remains urgent need of structural information on SL-CoV S to guide therapeutic countermeasure development. Among SL-CoVs, bat-derived WIV1 is capable of using as receptor the angiotensin converting enzyme 2 (ACE2) from a variety of mammals, thereby representing a prototype model for studying SL-CoV precursors to future pandemics. We present a WIV1 S cryo-EM structure in prefusion state which reveals molecular signatures reminiscent of the tightly-packed locked-1 conformation described for SARS-CoV-1 and SARS-CoV-2. To decipher the molecular basis for bat SL-CoV WIV1 host range tropism, we performed molecular dynamics (MD) simulations of WIV1 S-ACE2 interaction across reservoir bat, potentially intermediate hosts civet, raccoon dog and pangolin, and accidental human hosts. We found that, in all interactions, upon complex formation with ACE2, the linoleic acid responsible for locking the S receptor binding domain (RBD) dynamically persists in its binding pocket, however repositioning to potentially unlock the system. Complex formation between WIV1 S-RBD and ACE2 from different hosts was characterized in vitro by mass photometry and microscale thermophoresis, revealing that interaction is stronger with ACE2 from bat and human than other hosts, within the latter stronger for the Thr92Ile polymorphism correlated to higher SARS-CoV-2 infection susceptibility. These findings provide critical insights with crucial implications for pandemic preparedness.
History
DepositionMay 23, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60253.png

Downloads & links

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Map

FileDownload / File: emd_60253.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.77459 - 4.6579947
Average (Standard dev.)0.0006757074 (±0.08724329)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 436.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60253_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60253_half_map_2.map
Projections & Slices
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Sample components

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Entire : Bat SARS-like coronavirus (SL-CoV) WIV1 spike (S) glycoprotein

EntireName: Bat SARS-like coronavirus (SL-CoV) WIV1 spike (S) glycoprotein
Components
  • Complex: Bat SARS-like coronavirus (SL-CoV) WIV1 spike (S) glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: LINOLEIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Bat SARS-like coronavirus (SL-CoV) WIV1 spike (S) glycoprotein

SupramoleculeName: Bat SARS-like coronavirus (SL-CoV) WIV1 spike (S) glycoprotein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Bat SL-CoV WIV1 S glycoprotein in locked state
Source (natural)Organism: Bat SARS-like coronavirus WIV1

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bat SARS-like coronavirus WIV1
Molecular weightTheoretical: 134.758312 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKCLDFDDRT PPANTQFLSS HRGVYYPDDI FRSNVLHLVQ DHFLPFDSNV TRFITFGLNF DNPIIPFKDG IYFAATEKSN VIRGWVFGS TMNNKSQSVI IMNNSTNLVI RACNFELCDN PFFVVLKSNN TQIPSYIFNN AFNCTFEYVS KDFNLDLGEK P GNFKDLRE ...String:
MKCLDFDDRT PPANTQFLSS HRGVYYPDDI FRSNVLHLVQ DHFLPFDSNV TRFITFGLNF DNPIIPFKDG IYFAATEKSN VIRGWVFGS TMNNKSQSVI IMNNSTNLVI RACNFELCDN PFFVVLKSNN TQIPSYIFNN AFNCTFEYVS KDFNLDLGEK P GNFKDLRE FVFRNKDGFL HVYSGYQPIS AASGLPTGFN ALKPIFKLPL GINITNFRTL LTAFPPRPDY WGTSAAAYFV GY LKPTTFM LKYDENGTIT DAVDCSQNPL AELKCSVKSF EIDKGIYQTS NFRVAPSKEV VRFPNITNLC PFGEVFNATT FPS VYAWER KRISNCVADY SVLYNSTSFS TFKCYGVSAT KLNDLCFSNV YADSFVVKGD DVRQIAPGQT GVIADYNYKL PDDF TGCVL AWNTRNIDAT QTGNYNYKYR SLRHGKLRPF ERDISNVPFS PDGKPCTPPA FNCYWPLNDY GFYITNGIGY QPYRV VVLS FELLNAPATV CGPKLSTDLI KNQCVNFNFN GLTGTGVLTP SSKRFQPFQQ FGRDVSDFTD SVRDPKTSEI LDISPC SFG GVSVITPGTN TSSEVAVLYQ DVNCTDVPVA IHADQLTPSW RVHSTGNNVF QTQAGCLIGA EHVDTSYECD IPIGAGI CA SYHTVSSLRS TSQKSIVAYT MSLGADSSIA YSNNTIAIPT NFSISITTEV MPVSMAKTSV DCNMYICGDS TECANLLL Q YGSFCTQLNR ALSGIAVEQD RNTREVFAQV KQMYKTPTLK DFGGFNFSQI LPDPLKPTKR SFIEDLLFNK VTLADAGFM KQYGECLGDI NARDLICAQK FNGLTVLPPL LTDDMIAAYT AALVSGTATA GWTFGAGAAL QIPFAMQMAY RFNGIGVTQN VLYENQKQI ANQFNKAISQ IQESLTTTST ALGKLQDVVN QNAQALNTLV KQLSSNFGAI SSVLNDILSR LDKVEAEVQI D RLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC VLGQSKRVDF CGKGYHLMSF PQAAPHGVVF LHVTYVPSQE RN FTTAPAI CHEGKAYFPR EGVFVFNGTS WFITQRNFFS PQIITTDNTF VSGSCDVVIG IINNTVYDPL QPELDSFKEE LDK YFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQYI KGGSGYIPEA PRDGQAYVRK DGEW VLLST FLHHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #5: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 5 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMTris-HClTris(hydroxymethyl)aminomethane-hydrochloridic acid
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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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: 3.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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