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- EMDB-17082: Local refinement of the Human Coronavirus HKU1 spike glycoprotein... -

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Basic information

Entry
Database: EMDB / ID: EMD-17082
TitleLocal refinement of the Human Coronavirus HKU1 spike glycoprotein in complex with an alpha2,8-linked 9-O-acetylated disialoside (3-up state)
Map dataUnsharpened map
Sample
  • Complex: Trimeric spike glycoprotein
    • Protein or peptide: Spike glycoproteinSpike protein
KeywordsVirus / Coronavirus / HKU1 / Spike / Glycoprotein / Membrane fusion / 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 / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHuman coronavirus HKU1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDrulyte I / Hurdiss DL
Funding support Netherlands, China, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)VI.Veni.202.271 Netherlands
Chinese Scholarship Council2014-03250042 China
CitationJournal: Nature / Year: 2023
Title: Sialoglycan binding triggers spike opening in a human coronavirus.
Authors: Matti F Pronker / Robert Creutznacher / Ieva Drulyte / Ruben J G Hulswit / Zeshi Li / Frank J M van Kuppeveld / Joost Snijder / Yifei Lang / Berend-Jan Bosch / Geert-Jan Boons / Martin Frank ...Authors: Matti F Pronker / Robert Creutznacher / Ieva Drulyte / Ruben J G Hulswit / Zeshi Li / Frank J M van Kuppeveld / Joost Snijder / Yifei Lang / Berend-Jan Bosch / Geert-Jan Boons / Martin Frank / Raoul J de Groot / Daniel L Hurdiss /
Abstract: Coronavirus spike proteins mediate receptor binding and membrane fusion, making them prime targets for neutralizing antibodies. In the cases of severe acute respiratory syndrome coronavirus, severe ...Coronavirus spike proteins mediate receptor binding and membrane fusion, making them prime targets for neutralizing antibodies. In the cases of severe acute respiratory syndrome coronavirus, severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus, spike proteins transition freely between open and closed conformations to balance host cell attachment and immune evasion. Spike opening exposes domain S1, allowing it to bind to proteinaceous receptors, and is also thought to enable protein refolding during membrane fusion. However, with a single exception, the pre-fusion spike proteins of all other coronaviruses studied so far have been observed exclusively in the closed state. This raises the possibility of regulation, with spike proteins more commonly transitioning to open states in response to specific cues, rather than spontaneously. Here, using cryogenic electron microscopy and molecular dynamics simulations, we show that the spike protein of the common cold human coronavirus HKU1 undergoes local and long-range conformational changes after binding a sialoglycan-based primary receptor to domain S1. This binding triggers the transition of S1 domains to the open state through allosteric interdomain crosstalk. Our findings provide detailed insight into coronavirus attachment, with possibilities of dual receptor usage and priming of entry as a means of immune escape.
History
DepositionApr 7, 2023-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17082.png

Downloads & links

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Map

FileDownload / File: emd_17082.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 300 pix.
= 332.01 Å		1.11 Å/pix.
x 300 pix.
= 332.01 Å		1.11 Å/pix.
x 300 pix.
= 332.01 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.118
Minimum - Maximum-0.33210278 - 0.9559511
Average (Standard dev.)0.0027325915 (±0.016043784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 332.00998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17082_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_17082_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_17082_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric spike glycoprotein

EntireName: Trimeric spike glycoprotein
Components
  • Complex: Trimeric spike glycoprotein
    • Protein or peptide: Spike glycoproteinSpike protein

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Supramolecule #1: Trimeric spike glycoprotein

SupramoleculeName: Trimeric spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human coronavirus HKU1 / Strain: Caen1 / Location in cell: membrane
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus HKU1 / Strain: Caen1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAVIGDFN CTNFAINDLN TTIPRISEYV VDVSYGLGTY YILDRVYLNT TILFTGYFPK SGANFRDLSL KGTTKLSTLW YQKPFLSDFN NGIFSRVKNT KLYVNKTLYS EFSTIVIGSV FINNSYTIVV QPHNGVLEIT ACQYTMCEYP ...String:
MPMGSLQPLA TLYLLGMLVA SVLAVIGDFN CTNFAINDLN TTIPRISEYV VDVSYGLGTY YILDRVYLNT TILFTGYFPK SGANFRDLSL KGTTKLSTLW YQKPFLSDFN NGIFSRVKNT KLYVNKTLYS EFSTIVIGSV FINNSYTIVV QPHNGVLEIT ACQYTMCEYP HTICKSIGSS RNESWHFDKS EPLCLFKKNF TYNVSTDWLY FHFYQERGTF YAYYADSGMP TTFLFSLYLG TLLSHYYVLP LTCNAISSNT DNETLQYWVT PLSKRQYLLK FDDRGVITNA VDCSSSFFSE IQCKTKSLLP NTGVYDLSGF TVKPVATVHR RIPDLPDCDI DKWLNNFNVP SPLNWERKIF SNCNFNLSTL LRLVHTDSFS CNNFDESKIY GSCFKSIVLD KFAIPNSRRS DLQLGSSGFL QSSNYKIDTT SSSCQLYYSL PAINVTINNY NPSSWNRRYG FNNFNLSSHS VVYSRYCFSV NNTFCPCAKP SFASSCKSHK PPSASCPIGT NYRSCESTTV LDHTDWCRCS CLPDPITAYD PRSCSQKKSL VGVGEHCAGF GVDEEKCGVL DGSYNVSCLC STDAFLGWSY DTCVSNNRCN IFSNFILNGI NSGTTCSNDL LQPNTEVFTD VCVDYDLYGI TGQGIFKEVS AVYYNSWQNL LYDFNGNIIG FKDFVTNKTY NIFPCYAGRV SAAFHQNASS LALLYRNLKC SYVLNNISLA TQPYFDSYLG CVFNADNLTD YSVSSCALRM GSGFCVDYNS PSSSSSGGSG SSISASYRFV TFEPFNVSFV NDSIESVGGL YEIKIPTNFT IVGQEEFIQT NSPKVTIDCS LFVCSNYAAC HDLLSEYGTF CDNINSILDE VNGLLDTTQL HVADTLMQGV TLSSNLNTNL HFDVDNINFK SLVGCLGPHC GSSSRSFFED LLFDKVKLSD VGFVEAYNNC TGGSEIRDLL CVQSFNGIKV LPPILSESQI SGYTTAATVA AMFPPWSAAA GIPFSLNVQY RINGLGVTMD VLNKNQKLIA TAFNNALLSI QNGFSATNSA LAKIQSVVNS NAQALNSLLQ QLFNKFGAIS SSLQEILSRL DALEAQVQID RLINGRLTAL NAYVSQQLSD ISLVKLGAAL AMEKVNECVK SQSPRINFCG NGNHILSLVQ NAPYGLLFMH FSYKPISFKT VLVSPGLCIS GDVGIAPKQG YFIKHNDHWM FTGSSYYYPE PISDKNVVFM NTCSVNFTKA PLVYLNHSVP KLSDFESELS HWFKNQTSIA PNLTLNLHTI NATFLDLLIK RMKQIEDKIE EIESKQKKIE NEIARIKKIK LVPRGSLEWS HPQFEK

UniProtKB: Spike glycoprotein

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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

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMTris-HClTris
1.0 mMEDTAEthylenediaminetetraacetic acid
2.5 mMD-biotin
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsConcentration of protein (N-linked glycans not included due to glycan heterogeneity).

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 20 eV / Details: BioContinuum Imaging Filter
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4057 / Average exposure time: 2.68 sec. / Average electron dose: 46.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 956697
Startup modelType of model: OTHER / Details: Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1) / Details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 99174
FSC plot (resolution estimation)

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