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- EMDB-53513: Bottlenose dolphin coronavirus spike glycoprotein -

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ID or keywords:

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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


host cell 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 / 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: 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) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 500 pix.
= 418. Å		0.84 Å/pix.
x 500 pix.
= 418. Å		0.84 Å/pix.
x 500 pix.
= 418. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
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

Projections

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
FSC plot (resolution estimation)

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