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- EMDB-45402: Bat SARS-like Coronavirus RsSHC014 Spike Protein -

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Basic information

Entry
Database: EMDB / ID: EMD-45402
TitleBat SARS-like Coronavirus RsSHC014 Spike Protein
Map dataBat SARS-like Coronavirus RsSHC014 Spike protein ectodomain
Sample
  • Organelle or cellular component: Homotrimer of SHC014 CoV spike ectodomain
    • Protein or peptide: Spike glycoprotein
Keywordsspike / prefusion / coronavirus / bat / 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, SARS-CoV-like / 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 (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesBat SARS-like coronavirus RsSHC014
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAcreman CM / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: PLoS Pathog / Year: 2024
Title: Distinct pathways for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses.
Authors: Alexandra L Tse / Cory M Acreman / Inna Ricardo-Lax / Jacob Berrigan / Gorka Lasso / Toheeb Balogun / Fiona L Kearns / Lorenzo Casalino / Georgia L McClain / Amartya Mudry Chandran / ...Authors: Alexandra L Tse / Cory M Acreman / Inna Ricardo-Lax / Jacob Berrigan / Gorka Lasso / Toheeb Balogun / Fiona L Kearns / Lorenzo Casalino / Georgia L McClain / Amartya Mudry Chandran / Charlotte Lemeunier / Rommie E Amaro / Charles M Rice / Rohit K Jangra / Jason S McLellan / Kartik Chandran / Emily Happy Miller /
Abstract: Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from ...Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent bat CoVs to investigate their cell entry mechanisms. Unexpectedly, the successful recovery of rVSVs bearing the spike from SHC014-CoV, a SARS-like bat CoV, was associated with the acquisition of a novel substitution in the S2 fusion peptide-proximal region (FPPR). This substitution enhanced viral entry in both VSV and coronavirus contexts by increasing the availability of the spike receptor-binding domain to recognize its cellular receptor, ACE2. A second substitution in the S1 N-terminal domain, uncovered through the rescue and serial passage of a virus bearing the FPPR substitution, further enhanced spike:ACE2 interaction and viral entry. Our findings identify genetic pathways for adaptation by bat CoVs during spillover and host-to-host transmission, fitness trade-offs inherent to these pathways, and potential Achilles' heels that could be targeted with countermeasures.
History
DepositionJun 17, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45402.png

Downloads & links

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Map

FileDownload / File: emd_45402.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBat SARS-like Coronavirus RsSHC014 Spike protein ectodomain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 512 pix.
= 481.28 Å		0.94 Å/pix.
x 512 pix.
= 481.28 Å		0.94 Å/pix.
x 512 pix.
= 481.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.0442566 - 1.4582894
Average (Standard dev.)-0.000008001883 (±0.02587499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 481.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45402_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_45402_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 : Homotrimer of SHC014 CoV spike ectodomain

EntireName: Homotrimer of SHC014 CoV spike ectodomain
Components
  • Organelle or cellular component: Homotrimer of SHC014 CoV spike ectodomain
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: Homotrimer of SHC014 CoV spike ectodomain

SupramoleculeName: Homotrimer of SHC014 CoV spike ectodomain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bat SARS-like coronavirus RsSHC014
Molecular weightTheoretical: 421 KDa

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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: Bat SARS-like coronavirus RsSHC014
Molecular weightTheoretical: 140.564391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKLLVLVFAT LVSSYTIEKC LDFDDRTPPA NTQFLSSHRG VYYPDDIFRS NVLHLVQDHF LPFDSNVTRF ITFGLNFDNP IIPFRDGIY FAATEKSNVI RGWVFGSTMN NKSQSVIIMN NSTNLVIRAC NFELCDNPFF VVLKSNNTQI PSYIFNNAFN C TFEYVSKD ...String:
MKLLVLVFAT LVSSYTIEKC LDFDDRTPPA NTQFLSSHRG VYYPDDIFRS NVLHLVQDHF LPFDSNVTRF ITFGLNFDNP IIPFRDGIY FAATEKSNVI RGWVFGSTMN NKSQSVIIMN NSTNLVIRAC NFELCDNPFF VVLKSNNTQI PSYIFNNAFN C TFEYVSKD FNLDLGEKPG NFKDLREFVF RNKDGFLHVY SGYQPISAAS GLPTGFNALK PIFKLPLGIN ITNFRTLLTA FP PRPDYWG TSAAAYFVGY LKPTTFMLKY DENGTITDAV DCSQNPLAEL KCSVKSFEID KGIYQTSNFR VAPSKEVVRF PNI TNLCPF GEVFNATTFP SVYAWERKRI SNCVADYSVL YNSTSFSTFK CYGVSATKLN DLCFSNVYAD SFVVKGDDVR QIAP GQTGV IADYNYKLPD DFLGCVLAWN TNSKDSSTSG NYNYLYRWVR RSKLNPYERD LSNDIYSPGG QSCSAVGPNC YNPLR PYGF FTTAGVGHQP YRVVVLSFEL LNAPATVCGP KLSTDLIKNQ CVNFNFNGLT GTGVLTPSSK RFQPFQQFGR DVSDFT DSV RDPKTSEILD ISPCSFGGVS VITPGTNTSS EVAVLYQDVN CTDVPVAIHA DQLTPSWRVY STGNNVFQTQ AGCLIGA EH VDTSYECDIP IGAGICASYH TVSSLRSTSQ KSIVAYTMSL GADSSIAYSN NTIAIPTNFS ISITTEVMPV SMAKTSVD C NMYICGDSTE CANLLLQYGS FCTQLNRALS GIAVEQDRNT REVFAQVKQM YKTPTLKDFG GFNFSQILPD PLKPTKRSF IEDLLFNKVT LADAGFMKQY GECLGDINAR DLICAQKFNG LTVLPPLLTD DMIAAYTAAL VSGTATAGWT FGAGAALQIP FAMQMAYRF NGIGVTQNVL YENQKQIANQ FNKAISQIQE SLTTTSTALG KLQDVVNQNA QALNTLVKQL SSNFGAISSV L NDILSRLD KVEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQA AP HGVVFLH VTYVPSQERN FTTAPAICHE GKAYFPREGV FVFNGTSWFI TQRNFFSPQI ITTDNTFVSG SCDVVIGIIN NTV YDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESLIDLQEL GKYEQGSGYI PEAP RDGQA YVRKDGEWVL LSTFLGRSLE VLFQGPGHHH HHHHHSAWSH PQFEKGGGSG GGGSGGSAWS 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76442
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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