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- EMDB-39048: Local structure of HCoV-HKU1C spike in complex with glycan -

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Basic information

Entry
Database: EMDB / ID: EMD-39048
TitleLocal structure of HCoV-HKU1C spike in complex with glycan
Map data
Sample
  • Complex: HKU1C spike with sialoglycan
    • Protein or peptide: Spike glycoprotein
  • Ligand: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHKU1C / spike / TMPRSS2 / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to 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 / identical protein binding / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / 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, HKU1-like / 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 / Human coronavirus HKU1 (isolate N5)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsLu YC / Zhang X / Wang HF / Sun L / Yang HT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169109 China
CitationJournal: Cell / Year: 2024
Title: TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry.
Authors: Haofeng Wang / Xiaoce Liu / Xiang Zhang / Zhuoqian Zhao / Yuchi Lu / Dingzhe Pu / Zeyang Zhang / Jie Chen / Yajie Wang / Mengfei Li / Xuxue Dong / Yinkai Duan / Yujia He / Qiyu Mao / ...Authors: Haofeng Wang / Xiaoce Liu / Xiang Zhang / Zhuoqian Zhao / Yuchi Lu / Dingzhe Pu / Zeyang Zhang / Jie Chen / Yajie Wang / Mengfei Li / Xuxue Dong / Yinkai Duan / Yujia He / Qiyu Mao / Hangtian Guo / Haoran Sun / Yihan Zhou / Qi Yang / Yan Gao / Xiuna Yang / Hongzhi Cao / Luke Guddat / Lei Sun / Zihe Rao / Haitao Yang /
Abstract: The entry of coronaviruses is initiated by spike recognition of host cellular receptors, involving proteinaceous and/or glycan receptors. Recently, TMPRSS2 was identified as the proteinaceous ...The entry of coronaviruses is initiated by spike recognition of host cellular receptors, involving proteinaceous and/or glycan receptors. Recently, TMPRSS2 was identified as the proteinaceous receptor for HCoV-HKU1 alongside sialoglycan as a glycan receptor. However, the underlying mechanisms for viral entry remain unknown. Here, we investigated the HCoV-HKU1C spike in the inactive, glycan-activated, and functionally anchored states, revealing that sialoglycan binding induces a conformational change of the NTD and promotes the neighboring RBD of the spike to open for TMPRSS2 recognition, exhibiting a synergistic mechanism for the entry of HCoV-HKU1. The RBD of HCoV-HKU1 features an insertion subdomain that recognizes TMPRSS2 through three previously undiscovered interfaces. Furthermore, structural investigation of HCoV-HKU1A in combination with mutagenesis and binding assays confirms a conserved receptor recognition pattern adopted by HCoV-HKU1. These studies advance our understanding of the complex viral-host interactions during entry, laying the groundwork for developing new therapeutics against coronavirus-associated diseases.
History
DepositionFeb 6, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39048.png

Downloads & links

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Map

FileDownload / File: emd_39048.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.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-0.13690634 - 14.576084
Average (Standard dev.)-0.034224868 (±0.25083458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39048_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39048_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 : HKU1C spike with sialoglycan

EntireName: HKU1C spike with sialoglycan
Components
  • Complex: HKU1C spike with sialoglycan
    • Protein or peptide: Spike glycoprotein
  • Ligand: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HKU1C spike with sialoglycan

SupramoleculeName: HKU1C spike with sialoglycan / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human coronavirus HKU1

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus HKU1 (isolate N5) / Strain: isolate N5
Molecular weightTheoretical: 140.242453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIGDFNCTNS FINDYNKTIP RISEDVVDVS LGLGTYYVLN RVYLNTTLLF TGYFPKSGAN FRDLALKGSI YLSTLWYKPP FLSDFNNGI FSKVKNTKLY VNNTLYSEFS TIVIGSVFVN TSYTIVVQPH NGILEITACQ YTMCEYPHTV CKSKGSIRNE S WHIDSSEP ...String:
VIGDFNCTNS FINDYNKTIP RISEDVVDVS LGLGTYYVLN RVYLNTTLLF TGYFPKSGAN FRDLALKGSI YLSTLWYKPP FLSDFNNGI FSKVKNTKLY VNNTLYSEFS TIVIGSVFVN TSYTIVVQPH NGILEITACQ YTMCEYPHTV CKSKGSIRNE S WHIDSSEP LCLFKKNFTY NVSADWLYFH FYQERGVFYA YYADVGMPTT FLFSLYLGTI LSHYYVMPLT CNAISSNTDN ET LEYWVTP LSRRQYLLNF DEHGVITNAV DCSSSFLSEI QCKTQSFAPN TGVYDLSGFT VKPVATVYRR IPNLPDCDID NWL NNVSVP SPLNWERRIF SNCNFNLSTL LRLVHVDSFS CNNLDKSKIF GSCFNSITVD KFAIPNRRRD DLQLGSSGFL QSSN YKIDI SSSSCQLYYS LPLVNVTINN FNPSSWNRRY GFGSFNLSSY DVVYSDHCFS VNSDFCPCAD PSVVNSCAKS KPPSA ICPA GTKYRHCDLD TTLYVKNWCR CSCLPDPIST YSPNTCPQKK VVVGIGEHCP GLGINEEKCG TQLNHSSCFC SPDAFL GWS FDSCISNNRC NIFSNFIFNG INSGTTCSND LLYSNTEIST GVCVNYDLYG ITGQGIFKEV SAAYYNNWQN LLYDSNG NI IGFKDFLTNK TYTILPCYSG RVSAAFYQNS SSPALLYRNL KCSYVLNNIS FISQPFYFDS YLGCVLNAVN LTSYSVSS C DLRMGSGFCI DYALPSSGGS GSGISSPYRF VTFEPFNVSF VNDSVETVGG LFEIQIPTNF TIAGHEEFIQ TSSPKVTID CSAFVCSNYA ACHDLLSEYG TFCDNINSIL NEVNDLLDIT QLQVANALMQ GVTLSSNLNT NLHSDVDNID FKSLLGCLGS QCGSSSRSP LEDLLFNKVK LSDVGFVEAY NNCTGGSEIR DLLCVQSFNG IKVLPPILSE TQISGYTTAA TVAAMFPPWS A AAGVPFPL NVQYRINGLG VTMDVLNKNQ KLIANAFNKA LLSIQNGFTA TPSALAKIQS VVNANAQALN SLLQQLFNKF GA ISSSLQE ILSRLDPPEA QVQIDRLING RLTALNAYVS QQLSDITLIK AGASRAIEKV NECVKSQSPR INFCGNGNHI LSL VQNAPY GLLFIHFSYK PTSFKTVLVS PGLCLSGDRG IAPKQGYFIK QNDSWMFTGS SYYYPEPISD KNVVFMNSCS VNFT KAPFI YLNNSIPNLS DFEAELSLWF KNHTSIAPNL TFNSHINATF LDLYYEMNVI QESIKSLN

UniProtKB: Spike glycoprotein

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Macromolecule #4: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galac...

MacromoleculeName: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
type: ligand / ID: 4 / Number of copies: 1 / Formula: MJJ
Molecular weightTheoretical: 365.333 Da
Chemical component information

ChemComp-MJJ:
methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid

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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: 4 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120295
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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