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- EMDB-32825: Negative stain volume of the mono-GlcNAc-decorated SARS-CoV-2 Spike -

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Basic information

Entry
Database: EMDB / ID: EMD-32825
TitleNegative stain volume of the mono-GlcNAc-decorated SARS-CoV-2 Spike
Map datanegative stain volume of the mono-GlcNAc-decorated SARS-CoV-2 Spike
Sample
  • Complex: SARS-CoV-2 Spike
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 14.5 Å
AuthorsChen X / Huang H-Y
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108WIA0110239 Taiwan
CitationJournal: Sci Transl Med / Year: 2022
Title: Vaccination with SARS-CoV-2 spike protein lacking glycan shields elicits enhanced protective responses in animal models.
Authors: Han-Yi Huang / Hsin-Yu Liao / Xiaorui Chen / Szu-Wen Wang / Cheng-Wei Cheng / Md Shahed-Al-Mahmud / Yo-Min Liu / Arpita Mohapatra / Ting-Hua Chen / Jennifer M Lo / Yi-Min Wu / Hsiu-Hua Ma / ...Authors: Han-Yi Huang / Hsin-Yu Liao / Xiaorui Chen / Szu-Wen Wang / Cheng-Wei Cheng / Md Shahed-Al-Mahmud / Yo-Min Liu / Arpita Mohapatra / Ting-Hua Chen / Jennifer M Lo / Yi-Min Wu / Hsiu-Hua Ma / Yi-Hsuan Chang / Ho-Yang Tsai / Yu-Chi Chou / Yi-Ping Hsueh / Ching-Yen Tsai / Pau-Yi Huang / Sui-Yuan Chang / Tai-Ling Chao / Han-Chieh Kao / Ya-Min Tsai / Yen-Hui Chen / Chung-Yi Wu / Jia-Tsrong Jan / Ting-Jen Rachel Cheng / Kuo-I Lin / Che Ma / Chi-Huey Wong /
Abstract: A major challenge to end the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is to develop a broadly protective vaccine that elicits long-term immunity. As the key ...A major challenge to end the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is to develop a broadly protective vaccine that elicits long-term immunity. As the key immunogen, the viral surface spike (S) protein is frequently mutated, and conserved epitopes are shielded by glycans. Here, we revealed that S protein glycosylation has site-differential effects on viral infectivity. We found that S protein generated by lung epithelial cells has glycoforms associated with increased infectivity. Compared to the fully glycosylated S protein, immunization of S protein with N-glycans trimmed to the mono-GlcNAc-decorated state (S) elicited stronger immune responses and better protection for human angiotensin-converting enzyme 2 (hACE2) transgenic mice against variants of concern (VOCs). In addition, a broadly neutralizing monoclonal antibody was identified from S-immunized mice that could neutralize wild-type SARS-CoV-2 and VOCs with subpicomolar potency. Together, these results demonstrate that removal of glycan shields to better expose the conserved sequences has the potential to be an effective and simple approach for developing a broadly protective SARS-CoV-2 vaccine.
History
DepositionFeb 7, 2022-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.08
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32825.png

Downloads & links

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Map

FileDownload / File: emd_32825.map.gz / Format: CCP4 / Size: 4.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnegative stain volume of the mono-GlcNAc-decorated SARS-CoV-2 Spike
Voxel sizeX=Y=Z: 3.27 Å
Density
Contour LevelBy AUTHOR: 3.08 / Movie #1: 3.08
Minimum - Maximum-2.943897 - 20.647331
Average (Standard dev.)-0.10851496 (±1.6562594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions108108108
Spacing108108108
CellA=B=C: 353.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.273.273.27
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z353.160353.160353.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ416416416
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS108108108
D min/max/mean-2.94420.647-0.109

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 Spike

EntireName: SARS-CoV-2 Spike
Components
  • Complex: SARS-CoV-2 Spike

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Supramolecule #1: SARS-CoV-2 Spike

SupramoleculeName: SARS-CoV-2 Spike / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293
Molecular weightExperimental: 430 kDa/nm

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMTristris(hydroxymethyl)aminomethane
StainingType: NEGATIVE / Material: uranyl acetate / Details: 1%

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Number grids imaged: 1 / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22481
CTF correctionSoftware - Name: cisTEM
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM
Final 3D classificationNumber classes: 24 / Avg.num./class: 900 / Software - Name: cisTEM
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 12031

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