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- EMDB-39036: Structure of HCoV-HKU1C spike in the functionally anchored-1up co... -

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Basic information

Entry
Database: EMDB / ID: EMD-39036
TitleStructure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2
Map data
Sample
  • Complex: HKU1B-TMPRSS2 complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Transmembrane protease serine 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHKU1A / spike / TMPRSS2 / VIRAL PROTEIN
Function / homology
Function and homology information


transmembrane protease serine 2 / symbiont-mediated induction of syncytium formation / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell ...transmembrane protease serine 2 / symbiont-mediated induction of syncytium formation / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Transmembrane protease serine 2 / Spike glycoprotein
Similarity search - Component
Biological speciesHuman coronavirus HKU1 / Human coronavirus HKU1 (isolate N5) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsLu YC / Zhang X / Wang HF / Liu XC / 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 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39036.png

Downloads & links

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Map

FileDownload / File: emd_39036.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.001698308 - 1.9672494
Average (Standard dev.)0.002006097 (±0.033142652)
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_39036_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39036_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : HKU1B-TMPRSS2 complex

EntireName: HKU1B-TMPRSS2 complex
Components
  • Complex: HKU1B-TMPRSS2 complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Transmembrane protease serine 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HKU1B-TMPRSS2 complex

SupramoleculeName: HKU1B-TMPRSS2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 3 / 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 #2: Transmembrane protease serine 2

MacromoleculeName: Transmembrane protease serine 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: transmembrane protease serine 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.283629 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSKCSNSGI ECDSSGTCIN PSNWCDGVSH CPGGEDENRC VRLYGPNFIL QVYSSQRKSW HPVCQDDWNE NYGRAACRDM GYKNNFYSS QGIVDDSGST SFMKLNTSAG NVDIYKKLYH SDACSSKAVV SLRCIACGVN LNDDDDKIVG GESALPGAWP W QVSLHVQN ...String:
MGSKCSNSGI ECDSSGTCIN PSNWCDGVSH CPGGEDENRC VRLYGPNFIL QVYSSQRKSW HPVCQDDWNE NYGRAACRDM GYKNNFYSS QGIVDDSGST SFMKLNTSAG NVDIYKKLYH SDACSSKAVV SLRCIACGVN LNDDDDKIVG GESALPGAWP W QVSLHVQN VHVCGGSIIT PEWIVTAAHC VEKPLNNPWH WTAFAGILRQ SFMFYGAGYQ VEKVISHPNY DSKTKNNDIA LM KLQKPLT FNDLVKPVCL PNPGMMLQPE QLCWISGWGA TEEKGKTSEV LNAAKVLLIE TQRCNSRYVY DNLITPAMIC AGF LQGNVD SCQGDSGGPL VTSKNNIWWL IGDTSWGSGC AKAYRPGVYG NVMVFTDWIY RQMRADG

UniProtKB: Transmembrane protease serine 2

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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: 22 / 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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89212
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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