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- EMDB-37635: Cryo-EM structure of bat WIV1 spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-37635
TitleCryo-EM structure of bat WIV1 spike glycoprotein
Map data
Sample
  • Complex: WIV1 glycoprotein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsspike / 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, receptor-binding domain, SARS-CoV / Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Fibritin / Spike glycoprotein
Similarity search - Component
Biological speciesBat SARS-like coronavirus WIV1 / Enterobacteria phage T6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsWang X / Qiao S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2024
Title: Structural determinants of spike infectivity in bat SARS-like coronaviruses RsSHC014 and WIV1
Authors: Qiao S / Wang X
History
DepositionOct 1, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37635.png

Downloads & links

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Map

FileDownload / File: emd_37635.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 300.776 Å		1.07 Å/pix.
x 280 pix.
= 300.776 Å		1.07 Å/pix.
x 280 pix.
= 300.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0106
Minimum - Maximum-0.03664714 - 0.07791874
Average (Standard dev.)0.00026577557 (±0.0022800663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 300.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37635_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_37635_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 : WIV1 glycoprotein

EntireName: WIV1 glycoprotein
Components
  • Complex: WIV1 glycoprotein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: WIV1 glycoprotein

SupramoleculeName: WIV1 glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bat SARS-like coronavirus WIV1

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T6 (virus)
Molecular weightTheoretical: 140.747688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKLLVLVFAT LVSSYTIEKC LDFDDRTPPA NTQFLSSHRG VYYPDDIFRS NVLHLVQDHF LPFDSNVTRF ITFGLNFDNP IIPFKDGIY FAATEKSNVI RGWVFGSTMN NKSQSVIIMN NSTNLVIRAC NFELCDNPFF VVLKSNNTQI PSYIFNNAFN C TFEYVSKD ...String:
MKLLVLVFAT LVSSYTIEKC LDFDDRTPPA NTQFLSSHRG VYYPDDIFRS NVLHLVQDHF LPFDSNVTRF ITFGLNFDNP IIPFKDGIY 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 DFTGCVLAWN TRNIDATQTG NYNYKYRSLR HGKLRPFERD ISNVPFSPDG KPCTPPAFNC YWPLN DYGF YITNGIGYQP YRVVVLSFEL LNAPATVCGP KLSTDLIKNQ CVNFNFNGLT GTGVLTPSSK RFQPFQQFGR DVSDFT DSV RDPKTSEILD ISPCSFGGVS VITPGTNTSS EVAVLYQDVN CTDVPVAIHA DQLTPSWRVH 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 PPEAEVQIDR 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, Fibritin

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 19 / 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

Concentration0.3 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5x58

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59319
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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