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- EMDB-53513: Bottlenose dolphin coronavirus spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-53513
TitleBottlenose dolphin coronavirus spike glycoprotein
Map datalocal resolution filtered map
Sample
  • Complex: bottlenose dolphin coronavirus S glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsspike / glycoprotein / coronavirus / VIRAL PROTEIN
Function / homology
Function and homology information


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 / virion membrane / membrane
Similarity search - Function
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 speciesBottlenose dolphin coronavirus HKU22
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsHulswit RJG / Hurdiss DL
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Innovative Medicines Initiative101005077 Switzerland
CitationJournal: PLoS Pathog / Year: 2026
Title: Cetacean coronavirus spikes highlight S glycoprotein structural plasticity.
Authors: Ruben J G Hulswit / Tatiana M Shamorkina / Joline van der Lee / Floor Rosman / Lisanne S Wetzels / Frank J M van Kuppeveld / Joost Snijder / Berend Jan Bosch / Daniel L Hurdiss /
Abstract: Coronaviruses (CoVs) exhibit a remarkable ability for spill-over infections into naive host populations. While much research has focused on the spike (S) glycoproteins of zoonotic alpha- and ...Coronaviruses (CoVs) exhibit a remarkable ability for spill-over infections into naive host populations. While much research has focused on the spike (S) glycoproteins of zoonotic alpha- and betacoronaviruses, the S proteins of gamma- and deltacoronaviruses, which predominantly infect avian hosts, remain poorly understood. Here, we present high-resolution cryo-EM structures of S proteins from two distinct gammacoronaviruses (75.7% sequence identity) that atypically infect marine mammals and belong to the Gammacoronavirus delphinapteri species. The cryo-EM reconstructions reveal that the spikes exhibit a unique quaternary architecture that distinguishes them from other coronaviruses. The S protein features a previously unidentified, tripodal quaternary assembly of the S1 subunit, in which S1B domains are presented in an upright position while their putative receptor binding sites are shielded by extended loops from the S1A domain of the same protomers. Additionally, the CeCoV spike proteins have evolved an additional and unique ~200 residue N-terminal domain (S10). S10 lacks homology to known protein sequences but displays structural similarity to members of the cupin protein superfamily. This represents a remarkable case of coronaviral exaptation of a host protein integrated into the S glycoprotein. Moreover, glycoproteomic analyses reveal that CeCoV S proteins are extensively N-glycosylated (>100 N-glycans per trimer), with a notable abundance of high-mannose glycans on S10 and O-glycosylation sites within a mucin-like loop at the trimer apex, all contributing to a dense glycan shield and potentially masking immunogenic epitopes. These findings demonstrate the structural diversity and adaptability of CoV S proteins, including alternative quaternary assemblies, additional domains, and diverse glycosylation strategies, offering new insights into the evolutionary mechanisms that enable coronaviruses to expand their host range and establish infections in novel species.
History
DepositionApr 28, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53513.png

Downloads & links

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Map

FileDownload / File: emd_53513.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map
Voxel sizeX=Y=Z: 0.836 Å
Density
Contour LevelBy AUTHOR: 0.082
Minimum - Maximum-0.6153376 - 1.0365928
Average (Standard dev.)0.00040844938 (±0.012855172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 418.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_53513_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unsharpened half map A

Fileemd_53513_half_map_1.map
Annotationunsharpened half map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unsharpened half map B

Fileemd_53513_half_map_2.map
Annotationunsharpened half map B
Projections & Slices
AxesZYX

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Sample components

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Entire : bottlenose dolphin coronavirus S glycoprotein

EntireName: bottlenose dolphin coronavirus S glycoprotein
Components
  • Complex: bottlenose dolphin coronavirus S glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: bottlenose dolphin coronavirus S glycoprotein

SupramoleculeName: bottlenose dolphin coronavirus S glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bottlenose dolphin coronavirus HKU22

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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: Bottlenose dolphin coronavirus HKU22
Molecular weightTheoretical: 150.644297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AEEFLDFDLW PCDTCWNSSL LEENNTYTAA AFHQYGIIPF YYSINWTVVM NYSDGIYDYK WDDVAYNSSN YLAVNVSLVG RNCTANLNE TLTEYKGFDF KGFPFSCPDF NVTSIDHGMF GYLLQNVLLG RCTSHLCVVV IPQGRVFFQK DEMWWWSWGD R LGISSHFT ...String:
AEEFLDFDLW PCDTCWNSSL LEENNTYTAA AFHQYGIIPF YYSINWTVVM NYSDGIYDYK WDDVAYNSSN YLAVNVSLVG RNCTANLNE TLTEYKGFDF KGFPFSCPDF NVTSIDHGMF GYLLQNVLLG RCTSHLCVVV IPQGRVFFQK DEMWWWSWGD R LGISSHFT RFMVFDRNIT VIGIAGNFDL YRLGHDGCKY VTGQSCPGYN WMNVTRIPVV GQVCRWFYAD KDNLCNLTRV DN MPKTYYT AELARPATAS VIVDGAYKPV YTGKFVDDAL GPDYPCPTLS SLQASYVPGD CAIKDWVWIR SFDFKHTYFD AVY VGREEK FSLDAVQIIF RLKPNATYLG LPFCNETHTD KSSSAIIAYL IGGEFYSVDT STVVVETYNP HIPDPSATPT SAST TQSRT TIYGWQDLRS YNMSCVRFSY ELKRVMSVPL SMIRDVIIDV KKRVLSIDGF PVGSLLSDFE FRFSILAMND TYLAG LKYT TALITFDKGN VRNVIDCNSD SVFDKLRCDL QTDVMSDGFY PVNIKTNEAE ENATFIDVEA TLANLSLEVF VSSPSH SPA CLLKSYKCVD TRYFYLQNYT YSCADNGIND AASSAYCEGR MDTFNKFGVN GLDFRGKCPF SASKVNTGLI FDKICFG VY EQGCQADKVC NFGFYFDDVV FNQYGNKVYY KRQDLGFIDY QFGTLFKNSL VQPNVIQDGC HDYDIYGYKG TGFVKPFF D YSYLNMGGLI MLDSGGFPAV FRHNFALYEV TQCTREVAQL AVASNNALGC YLPKQVNIEG LNDTVDCNIT GVFKYCSYG SIQAALSEEV QINVCNPSLM MENSHCINLK GSFMVNEPSV TLNSTTYQPL LGVSGEVVLP RTLMLHTTTE FIQTHSPKIV IDCNKYVCG SSERCRRILI KYGGFCESII RLLNGVNMAD DVSVTDFLDN LNSFDNISIS LQSLNDSFGS FDGYGFQKFL P KSFDFGSG DPRQSRSTIE DLLFDKVTTV GLGTVDADYD KCTKGLSVAD LVCAQYYNGI MVLPGVADAE KMAMYTGALV GG MALGGIT AAASIPFATQ IQARVNYLAL TQNAIQENQK IIVQQFNKAI DSMTSAFESV NAGFSAVSSA ITEIQNTVNA QSQ ALTKLL GQLNYNFGAT TSSIKELYER LAPPEADIQV DRLINGRLTA LSAFVAARQV EASRVASQRV LAAEKINECV KSTS NRYGF CGNGTHIISF PQNAPNGMLF VHFSLVPNET ITVYGIIGLC LNNSIGIVPA KDRGIFIKCS NGSYCPEFEN SFNMT KDGN VTFPFAITSR EQYNPRQITT GDIQMLTSCN SSYTHIEWSQ LPLVAPPYKD FDQEFEELYE KWNY

UniProtKB: Spike glycoprotein

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 36 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
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: OTHER / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 321116
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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