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- EMDB-70904: Cryo-EM structure of HCoV-OC43-C2 Spike glycoprotein in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-70904
TitleCryo-EM structure of HCoV-OC43-C2 Spike glycoprotein in complex with 9O-acetyl GD3 sialoglycan (Local refined D1 domain)
Map data
Sample
  • Complex: Human coronavirus OC43 spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
  • Ligand: water
Keywordsspike glycoprotein ectodomain / proline stablized / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment 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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 speciesHuman coronavirus OC43
Methodsingle particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsJin M / Rini JM
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2026
Title: OC43 clinical isolate spike proteins have distinct carbohydrate-binding properties.
Authors: Zaky Hassan / Min Jin / Ying Liu / Zhijie Li / Alan H M Wong / Marc Desforges / Adam Forman / Mark Nitz / Tarini Gunawardena / Theo J Moraes / Masahiro Narimatsu / Jeffrey L Wrana / Hai Yu / ...Authors: Zaky Hassan / Min Jin / Ying Liu / Zhijie Li / Alan H M Wong / Marc Desforges / Adam Forman / Mark Nitz / Tarini Gunawardena / Theo J Moraes / Masahiro Narimatsu / Jeffrey L Wrana / Hai Yu / Xi Chen / James M Rini /
Abstract: The human coronavirus HCoV-OC43 (OC43) is the most widespread of the four common cold-causing seasonal coronaviruses, and tissue culture-adapted strains of it have been used for ~50 years. ...The human coronavirus HCoV-OC43 (OC43) is the most widespread of the four common cold-causing seasonal coronaviruses, and tissue culture-adapted strains of it have been used for ~50 years. Nevertheless, clinical isolates of OC43 differ from tissue culture-adapted OC43 in ways that call into question the value of the latter as a model. Among these are differences in their entry mechanisms and the activities of their hemagglutinin-esterases (HE). We now show that the spike proteins of OC43 clinical isolates differ from that of the tissue culture-adapted reference strain (OC43-Lab) in their carbohydrate-binding properties and ability to bind mucins, decoy receptors cleaved by the HE. We also show that, unlike HCoV-HKU1 (HKU1), they do not bind with high affinity and specificity the 9-O-acetylated α2-8-linked disialic acid moiety implicated in viral entry for OC43-Lab and HKU1. The spike proteins of the OC43 clinical isolates possess two inserts, not found in OC43-Lab, that flank the carbohydrate-binding site. Our structural analysis of a representative clinical isolate shows that insert-2 is a determinant of these specificity differences and that the carbohydrate-binding site undergoes conformational changes on carbohydrate binding. These structural features are shared by HKU1 and suggest common mechanisms for adaptation to the human sialoglycome.
History
DepositionMay 30, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70904.png

Downloads & links

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Map

FileDownload / File: emd_70904.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 329.6 Å		0.82 Å/pix.
x 400 pix.
= 329.6 Å		0.82 Å/pix.
x 400 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.5060532 - 1.0188857
Average (Standard dev.)0.000049528342 (±0.010952703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70904_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_70904_half_map_1.map
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Half map: #2

Fileemd_70904_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human coronavirus OC43 spike glycoprotein

EntireName: Human coronavirus OC43 spike glycoprotein
Components
  • Complex: Human coronavirus OC43 spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
  • Ligand: water

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Supramolecule #1: Human coronavirus OC43 spike glycoprotein

SupramoleculeName: Human coronavirus OC43 spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Ectodomain generated by recombinant expression in HEK293 Freestyle cells
Source (natural)Organism: Human coronavirus OC43

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus OC43
Molecular weightTheoretical: 147.597812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIGDLNCTLD PRLKGSFNNR DTGPPSISID TVDVTNGLGT YYVLDRVYLN TTLFLNGYYP TSGSTYRNMA LKGTDLLSTL WFKPPFLSD FINGIFAKVK NTKVFKDGVM YSEFPAITIG STFVNTSYSV VVQPRTINST QDGVNKLQGL LEVSVCQYNM C EYPHTICH ...String:
VIGDLNCTLD PRLKGSFNNR DTGPPSISID TVDVTNGLGT YYVLDRVYLN TTLFLNGYYP TSGSTYRNMA LKGTDLLSTL WFKPPFLSD FINGIFAKVK NTKVFKDGVM YSEFPAITIG STFVNTSYSV VVQPRTINST QDGVNKLQGL LEVSVCQYNM C EYPHTICH PNLGNHFKEL WHYDTGVVSC LYKRNFTYDV NATYLYFHFY QEGGTFYAYF TDTGFVTKFL FNVYLGMALS HY YVMPLTC IRRPKDGFSL EYWVTPLTPR QYLLAFNQDG IIFNAVDCMS DFMSEIKCKT QSIAPPTGVY ELNGYTVQPV ADV YRRKPD LPNCNIEAWL NDKSVPSPLN WERKTFSNCN FNMSSLMSFI QADSFTCNNI DAAKIYGMCF SSITIDKFAI PNRR KVDLQ LGNLGYLQSS NYRIDTTATS CQLYYNLPAA NVSVSRFNPS TWNKRFGFIE DSVFVPQPTG VFTNHSVVYA QHCFK APKN FCPCSSCPGK NNGIGTCPAG TNSLTCDNLC TLDPITLKAP DTYKCPQSKS LVGIGEHCSG LAVKSDYCGN NSCTCQ PQA FLGWSADSCL QGDKCNIFAN FILHDVNNGL TCSTDLQKAN TEIELGVCVN YDLYGISGQG IFVEVNATYY NSWQNLL YD SNGNLYGFRD YITNRTFMIH SCYSGRVSAA YHANSSEPAL LFRNIKCNYV FNNSLTRQLQ PINYSFDSYL GCVVNAYN S TAISVQTCDL TVGSGYCVDY SKNRRSRRAI TTGYRFTNFE PFTVNSVNDS LEPVGGLYEI QIPSEFTIGN MEEFIQTSS PKVTIDCAAF VCGDYAACKL QLVEYGSFCD NINAILTEVN ELLDTTQLQV ANSLMNGVTL STKLKDGVNF NVDDINFSPV LGCLGSECS KASSRSAIED LLFDKVKLSD VGFVEAYNNC TGGAEIRDLI CVQSYKGIKV LPPLLSENQI SGYTLAATSA S LFPPWTAA AGVPFYLNVQ YRINGLGVTM DVLSQNQKLI ANAFNNALHA IQQGFDAPNS ALVKIQAVVN ANAEALNNLL QQ LSNRFGA ISASLQEILS RLDPPEAEAQ IDRLINGRLT ALNAYVSQQL SDSTLVKFSA AQAMEKVNEC VKSQSSRINF CGN GNHIIS LVQNAPYGLY FIHFNYVPTK YVTAKVSPGL CIAGNRGIAP KSGYFVNVNN TWMYTGSGYY YPEPITENNV VVMS TCAVN YTKAPYVMLN TSIPNLPDFK EELDQWFKNQ TSVALDLSLD YINVTFLDLQ VEMNRLQEAI KVLNHSYINL KDIGT YEYY VKSGGYIPEA PRDGQAYVRK DGEWVLLSTF LNSGRAHHHH HH

UniProtKB: Spike glycoprotein

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alp...

MacromoleculeName: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1AR1
Molecular weightTheoretical: 642.561 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 103 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
50.0 mMNaClNaCl
GridModel: C-flat-2/2 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 20
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
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
Details: A initial 3D map was generated by ab-initio reconstruction in cryoSPARC v4
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4438041
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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