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- EMDB-41149: Cryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1... -

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Basic information

Entry
Database: EMDB / ID: EMD-41149
TitleCryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1 in Closed Conformation
Map data
Sample
  • Virus: Bat SARS-like coronavirus WIV1
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
  • Ligand: water
KeywordsSpike / Glycoprotein / Coronavirus / 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 / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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 WIV1
Methodsingle particle reconstruction / cryo EM / Resolution: 1.88 Å
AuthorsBostina M / Hills FR / Eruera A
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: PLoS Pathog / Year: 2024
Title: Variation in structural motifs within SARS-related coronavirus spike proteins.
Authors: Francesca R Hills / Alice-Roza Eruera / James Hodgkinson-Bean / Fátima Jorge / Richard Easingwood / Simon H J Brown / James C Bouwer / Yi-Ping Li / Laura N Burga / Mihnea Bostina /
Abstract: SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species ...SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments.
History
DepositionJun 29, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41149.png

Downloads & links

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Map

FileDownload / File: emd_41149.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 450 pix.
= 374.4 Å		0.83 Å/pix.
x 450 pix.
= 374.4 Å		0.83 Å/pix.
x 450 pix.
= 374.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0677
Minimum - Maximum-0.39450464 - 0.8541495
Average (Standard dev.)-0.000052073836 (±0.01452661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41149_half_map_1.map
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Half map: #1

Fileemd_41149_half_map_2.map
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Sample components

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Entire : Bat SARS-like coronavirus WIV1

EntireName: Bat SARS-like coronavirus WIV1
Components
  • Virus: Bat SARS-like coronavirus WIV1
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
  • Ligand: water

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Supramolecule #1: Bat SARS-like coronavirus WIV1

SupramoleculeName: Bat SARS-like coronavirus WIV1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 1415852 / Sci species name: Bat SARS-like coronavirus WIV1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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 WIV1
Molecular weightTheoretical: 122.841266 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: KCLDFDDRTP PANTQFLSSH RGVYYPDDIF RSNVLHLVQD HFLPFDSNVT RFITFGLNFD NPIIPFKDGI YFAATEKSNV IRGWVFGST MNNKSQSVII MNNSTNLVIR ACNFELCDNP FFVVLKSNNT QIPSYIFNNA FNCTFEYVSK DFNLDLGEKP G NFKDLREF ...String:
KCLDFDDRTP PANTQFLSSH RGVYYPDDIF RSNVLHLVQD HFLPFDSNVT RFITFGLNFD NPIIPFKDGI YFAATEKSNV IRGWVFGST MNNKSQSVII MNNSTNLVIR ACNFELCDNP FFVVLKSNNT QIPSYIFNNA FNCTFEYVSK DFNLDLGEKP G NFKDLREF VFRNKDGFLH VYSGYQPISA ASGLPTGFNA LKPIFKLPLG INITNFRTLL TAFPPRPDYW GTSAAAYFVG YL KPTTFML KYDENGTITD AVDCSQNPLA ELKCSVKSFE IDKGIYQTSN FRVAPSKEVV RFPNITNLCP FGEVFNATTF PSV YAWERK RISNCVADYS VLYNSTSFST FKCYGVSATK LNDLCFSNVY ADSFVVKGDD VRQIAPGQTG VIADYNYKLP DDFT GCVLA WNTRNIDATQ TGNYNYKYRS LRHGKLRPFE RDISNVPFSP DGKPCTPPAF NCYWPLNDYG FYITNGIGYQ PYRVV VLSF ELLNAPATVC GPKLSTDLIK NQCVNFNFNG LTGTGVLTPS SKRFQPFQQF GRDVSDFTDS VRDPKTSEIL DISPCS FGG VSVITPGTNT SSEVAVLYQD VNCTDVPVAI HADQLTPSWR VHSTGNNVFQ TQAGCLIGAE HVDTSYECDI PIGAGIC AS YHTVSSLRST SQKSIVAYTM SLGADSSIAY SNNTIAIPTN FSISITTEVM PVSMAKTSVD CNMYICGDST ECANLLLQ Y GSFCTQLNRA LSGIAVEQDR NTREVFAQVK QMYKTPTLKD FGGFNFSQIL PDPLKPTKRS FIEDLLFNKV TLADAGFMK QYGECLGDIN ARDLICAQKF NGLTVLPPLL TDDMIAAYTA ALVSGTATAG WTFGAGAALQ IPFAMQMAYR FNGIGVTQNV LYENQKQIA NQFNKAISQI QESLTTTSTA LGKLQDVVNQ NAQALNTLVK QLSSNFGAIS SVLNDILSRL DKVEAEVQID R LITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QAAPHGVVFL HVTYVPSQER NF TTAPAIC HEGKAYFPRE GVFVFNGTSW FITQRNFFSP QIITTDNTFV SGSCDVVIGI INNTVYDPLQ PE

UniProtKB: Spike glycoprotein

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 7 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 207 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 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:

7e7b

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 800000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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