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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: To Be Published
Title: Atypical features of cetacean coronavirus spikes highlight structural plasticity of the S glycoprotein
Authors: Hulswit RJG / Hurdiss DL
History
DepositionApr 28, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 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
Contrast
Others
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
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map A

Fileemd_53512_half_map_1.map
Annotationunfiltered half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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