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- EMDB-53512: Beluga whale coronavirus spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-53512
TitleBeluga whale coronavirus spike glycoprotein
Map datalocal resolution filtered map
Sample
  • Complex: Beluga whale coronavirus spike glycoprotein
    • Protein or peptide: Spike protein
  • 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
Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-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
Biological speciesBeluga whale coronavirus SW1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 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) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53512.png

Downloads & links

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Map

FileDownload / File: emd_53512.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 384 pix.
= 418. Å		1.09 Å/pix.
x 384 pix.
= 418. Å		1.09 Å/pix.
x 384 pix.
= 418. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08854 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.425
Minimum - Maximum-2.385028 - 3.6435802
Average (Standard dev.)0.001682068 (±0.054608896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 418.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_53512_additional_1.map
AnnotationUnsharpened map
Projections & Slices
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Half map: unfiltered half map A

Fileemd_53512_half_map_1.map
Annotationunfiltered half map A
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map B

Fileemd_53512_half_map_2.map
Annotationunfiltered half map B
Projections & Slices
AxesZYX

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Sample components

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Entire : Beluga whale coronavirus spike glycoprotein

EntireName: Beluga whale coronavirus spike glycoprotein
Components
  • Complex: Beluga whale coronavirus spike glycoprotein
    • Protein or peptide: Spike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Beluga whale coronavirus spike glycoprotein

SupramoleculeName: Beluga whale coronavirus spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Beluga whale coronavirus SW1

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Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Beluga whale coronavirus SW1
Molecular weightTheoretical: 153.930609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IDEGLWPAGM WYSHLLQENN TYTVAAFQEH AILPSYVNNN WTVITNFTAE NATQLEWDDP YYNSTLFSYV NITMVGDNCI GNFTNRTLG ELGDIDYFPF NCTNVTNEFR TNYGYFIQNV MVARCLSSLC AVIIPKGRVF FEKNEMWWWS WQDRYQPGNY T FRHERFMS ...String:
IDEGLWPAGM WYSHLLQENN TYTVAAFQEH AILPSYVNNN WTVITNFTAE NATQLEWDDP YYNSTLFSYV NITMVGDNCI GNFTNRTLG ELGDIDYFPF NCTNVTNEFR TNYGYFIQNV MVARCLSSLC AVIIPKGRVF FEKNEMWWWS WQDRYQPGNY T FRHERFMS LSQNITVIGL AGNFSLFGLG QTININSASY DWGTVIRGRL DDRICELQMT GADLCNLTRV DTSSDAFYTA GL VRPASAA LIADGAYKPI FTGVFHDNET HQVLYENATI KPSVRSFQVK NNDFDALYVG RKEKFSIDAV TIIFRLKETS TYL DLPFCN ETRVDKSDKA IIGYLIGGDF YSVDVSSIVI ERYNPPQPNA TSIPTTISTV STTTSGWEDL RSLNMSCVRF DYKL KKVMS VPLPMVKAFI IDFKQRQLAI DGFPVGALIA DFEFRFSIVA MPQTFISTLN YTTALVTFDK GNVRSVIDCN SEKPF DRLR CDLQTDVVSD GFYPVNIKTN EAKENTTFID VPATLANLTL EVFVSSPEQS PACVIKSYKC VDTRYFYISD YSYSCA ENG IPNDAAGAAY CRGVLDQINN YGVRGMDFKG KCPFAGSKVN SGLTFDKICF GVYEQGCQSD KACRFGFYFD NVQFSQY GN KLYYKPQDLG FIDYQFGTLF KNSLVQSNII QEGCHDYDIY GYKGTGVVKP FSDYSYLQTG GLIMLDSGGF PSLFRYNF A LYEVTQCTRE VAQLAVASNN AIGYYLPKQV TIDGVNASTS CNTTGAFKYC YYDDVIHVGR DVSNVTINVC NPSLMMENS HCINIQGNFM VNEPAITFNS TQYQPLLGVS GDVQLPRTLM LHTTTEFIQT HSPKIVIDCT KYVCGSSERC RRILVKYGGF CESIMRLLN GVNMADDVSV TDFLDNFNSF DNISVSLQNL NASFGQFEGY GFQKFLPKSF DFDGSDPRDA RSTIEDILFD K VTTVGLGT VDADYDKCTK GLSVADLVCA QYYNGIMVLP GVADAEKMAM YTGALVGGMV LGGITSAAAI PFATQIQARV NY LALTQNA IQENQKIIVQ QFNKAIDSMT SAFQSVNEGF SAVSSAITEV QNAVNAQSQA LTKLLGQLNY NFGATTSSIK ELY ERLAPP EADVQVDRLI NGRLTALSAF VAARQVEAAK VASQRVLAAE KINECVKSTS NRYGFCGNGA HIISFPQNAP NGML FVHFS LVPNETITVK GIIGLCLNNS IGIVPAKDRG MFIQCSNGTY CPEFENSFNE SKNGNVTFPF AITSREQYNP RQITT GDIQ MLTSCNSGYT HIEWSQLPLV APPYDDFDKE FDKLYEKWNY TLEELEKLNV TFPYLNVSEQ IDIINSAMEN IKSQIQ NLN SSYIDLEWLN KYER

UniProtKB: Spike protein

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 30 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 687529
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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