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- EMDB-48804: Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31... -

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Basic information

Entry
Database: EMDB / ID: EMD-48804
TitleCryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31VPR34 to GGGG)
Map data
Sample
  • Complex: Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31VPR34 to GGGG)
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHCoV-HKU1 spike 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, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHuman coronavirus HKU1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsJin M / Rini JM
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2025
Title: Human coronavirus HKU1 spike structures reveal the basis for sialoglycan specificity and carbohydrate-promoted conformational changes.
Authors: Min Jin / Zaky Hassan / Zhijie Li / Ying Liu / Aleksandra Marakhovskaia / Alan H M Wong / Adam Forman / Mark Nitz / Michel Gilbert / Hai Yu / Xi Chen / James M Rini /
Abstract: The human coronavirus HKU1 uses both sialoglycoconjugates and the protein transmembrane serine protease 2 (TMPRSS2) as receptors. Carbohydrate binding leads to the spike protein up conformation ...The human coronavirus HKU1 uses both sialoglycoconjugates and the protein transmembrane serine protease 2 (TMPRSS2) as receptors. Carbohydrate binding leads to the spike protein up conformation required for TMPRSS2 binding, an outcome suggesting a distinct mechanism for driving fusion of the viral and host cell membranes. Nevertheless, the conformational changes promoted by carbohydrate binding have not been fully elucidated and the basis for HKU1's carbohydrate binding specificity remains unknown. Reported here are high resolution cryo-EM structures of the HKU1 spike protein trimer in its apo form and in complex with the carbohydrate moiety of a candidate carbohydrate receptor, the 9-O-acetylated GD3 ganglioside. The structures show that the spike monomer can exist in four discrete conformational states and that progression through them would promote the up conformation upon carbohydrate binding. We also show that a six-amino-acid insert is a determinant of HKU1's specificity for gangliosides containing a 9-O-acetylated α2-8-linked disialic acid moiety and that HKU1 shows weak affinity for the 9-O-acetylated sialic acids found on decoy receptors such as mucins.
History
DepositionJan 24, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48804.png

Downloads & links

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Map

FileDownload / File: emd_48804.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 256 pix.
= 288. Å		1.13 Å/pix.
x 256 pix.
= 288. Å		1.13 Å/pix.
x 256 pix.
= 288. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.53614736 - 1.3511219
Average (Standard dev.)0.0005658801 (±0.03512765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48804_msk_1.map
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Half map: #1

Fileemd_48804_half_map_1.map
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Half map: #2

Fileemd_48804_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31...

EntireName: Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31VPR34 to GGGG)
Components
  • Complex: Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31VPR34 to GGGG)
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31...

SupramoleculeName: Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31VPR34 to GGGG)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Ectodomain generated by recombinant expression in HEK293 Freestyle cells
Source (natural)Organism: Human coronavirus HKU1
Molecular weightTheoretical: 457.593 KDa

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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 HKU1
Molecular weightTheoretical: 150.532578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIGDFNCTNF AINDLNTTVP GISEYVVDVS YGLGTYYILD RVYLNTTILF TGYFPKSGAN FRDLSLKGTT YLSTLWYQKP FLSDFNNGI FSRVKNTKLY VNKTLYSEFS TIVIGSVFIN NSYTIVVQPH NGVLEITACQ YTMCEYPHTI CKSKGSSRNE S WHFDKSEP ...String:
VIGDFNCTNF AINDLNTTVP GISEYVVDVS YGLGTYYILD RVYLNTTILF TGYFPKSGAN FRDLSLKGTT YLSTLWYQKP FLSDFNNGI FSRVKNTKLY VNKTLYSEFS TIVIGSVFIN NSYTIVVQPH NGVLEITACQ YTMCEYPHTI CKSKGSSRNE S WHFDKSEP LCLFKKNFTY NVSTDWLYFH FYQERGTFYA YYADSGMPTT FLFSLYLGTL LSHYYVLPLT CNAISSNTDN ET LQYWVTP LSKRQYLLKF DNRGVITNAV DCSSSFFSEI QCKTKSLLPN TGVYDLSGFT VKPVATVHRR IPDLPDCDID KWL NNFNVP SPLNWERKIF SNCNFNLSTL LRLVHTDSFS CNNFDESKIY GSCFKSIVLD KFAIPNSRRS DLQLGSSGFL QSSN YKIDT TSSSCQLYYS LPAINVTINN YNPSSWNRRY GFNNFNLSSH SVVYSRYCFS VNNTFCPCAK PSFASSCKSH KPPSA SCPI GTNYRSCEST TVLDHTDWCR CSCLPDPITA YDPRSCSQKK SLVGVGEHCA GFGVDEEKCG VLDGSYNVSC LCSTDA FLG WSYDTCVSNN RCNIFSNFIL NGINSGTTCS NDLLQPNTEV FTDVCVDYDL YGITGQGIFK EVSAVYYNSW QNLLYDS NG NIIGFKDFVT NKTYNIFPCY AGRVSAAFHQ NASSLALLYR NLKCSYVLNN ISLTTQPYFD SYLGCVFNAD NLTDYSVS S CALRMGSGFC VDYNSPSSSS SRRKRRSISA SYRFVTFEPF NVSFVNDSIE SVGGLYEIKI PTNFTIVGQE EFIQTNSPK VTIDCSLFVC SNYAACHDLL SEYGTFCDNI NSILDEVNGL LDTTQLHVAD TLMQGVTLSS NLNTNLHFDV DNINFKSLVG CLGPHCGSS SRSFFEDLLF DKVKLSDVGF VEAYNNCTGG SEIRDLLCVQ SFNGIKVLPP ILSESQISGY TTAATVAAMF P PWSAAAGI PFSLNVQYRI NGLGVTMDVL NKNQKLIATA FNNALLSIQN GFSAPNSALA KIQSVVNSNA QALNSLLQQL FN KFGAISS SLQEILSRLD PPEAQVQIDR LINGRLTALN AYVSQQLSDI SLVKFGAALA MEKVNECVKS QSPRINFCGN GNH ILSLVQ NAPYGLLFMH FSYKPISFKT VLVSPGLCIS GDVGIAPKQG YFIKHNDHWM FTGSSYYYPE PISDKNVVFM NTCS VNFTK APLVYLNHSV PKLSDFESEL SHWFKNQTSI APNLTLNLHT INATFLDLYY EMNLIQESIK SLNNSYINLK DIGTY EMYV KSGGYIPEAP RDGQAYVRKD GEWVLLSTFL NSGRAHHHHH HGAGGLNDIF EAQKIEWHED TAAA

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / 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

Concentration1.15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
50.0 mMNaClNaCl
GridModel: C-flat-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 GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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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: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 302976
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9n13:
Cryo-EM structure of HCoV-HKU1 glycoprotein D1 Domain (mutant T31VPR34 to GGGG)

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