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- EMDB-44885: Cryo-EM density map of HKU1 spike glycoprotein D1 domain in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-44885
TitleCryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3 sialoglycan (Down_alt state, locally refined)
Map data
Sample
  • Complex: Human coronavirus HKU1 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
KeywordsHKU1 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: 2.39 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
DepositionMay 14, 2024-
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_44885.png

Downloads & links

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Map

FileDownload / File: emd_44885.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 352 pix.
= 362.56 Å		1.03 Å/pix.
x 352 pix.
= 362.56 Å		1.03 Å/pix.
x 352 pix.
= 362.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2788291 - 3.6390445
Average (Standard dev.)-0.00036454608 (±0.038356137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 362.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44885_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44885_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44885_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human coronavirus HKU1 spike glycoprotein

EntireName: Human coronavirus HKU1 spike glycoprotein
Components
  • Complex: Human coronavirus HKU1 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

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Supramolecule #1: Human coronavirus HKU1 spike glycoprotein

SupramoleculeName: Human coronavirus HKU1 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 HKU1
Molecular weightTheoretical: 152.531 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: 150.632734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIGDFNCTNF AINDLNTTVP RISEYVVDVS YGLGTYYILD RVYLNTTILF TGYFPKSGAN FRDLSLKGTT YLSTLWYQKP FLSDFNNGI FSRVKNTKLY VNKTLYSEFS TIVIGSVFIN NSYTIVVQPH NGVLEITACQ YTMCEYPHTI CKSKGSSRNE S WHFDKSEP ...String:
VIGDFNCTNF AINDLNTTVP RISEYVVDVS 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 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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 #6: 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: 6 / Number of copies: 1 / Formula: A1AR1
Molecular weightTheoretical: 642.561 Da

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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-2/2 / 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

MicroscopeFEI TITAN 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: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000
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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1130290
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsSymmetry-expanded particles are classified focused at D1 domain. Particles with D1 domain in active state are used in final local refinement and reconstruction with D1-only Mask.
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9bta:
Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3 sialoglycan (Down_alt state, locally refined)

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