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- EMDB-38701: XBB.1.5-K356T S-trimer (3 RBDs down) -

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Basic information

Entry
Database: EMDB / ID: EMD-38701
TitleXBB.1.5-K356T S-trimer (3 RBDs down)
Map data
Sample
  • Complex: XBB.1.5-K356T S-trimer (3 RBDs down)
KeywordsSpike / SARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.37 Å
AuthorsYue C / Liu P
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Natl Sci Rev / Year: 2024
Title: Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity.
Authors: Pan Liu / Can Yue / Bo Meng / Tianhe Xiao / Sijie Yang / Shuo Liu / Fanchong Jian / Qianhui Zhu / Yuanling Yu / Yanyan Ren / Peng Wang / Yixin Li / Jinyue Wang / Xin Mao / Fei Shao / Youchun ...Authors: Pan Liu / Can Yue / Bo Meng / Tianhe Xiao / Sijie Yang / Shuo Liu / Fanchong Jian / Qianhui Zhu / Yuanling Yu / Yanyan Ren / Peng Wang / Yixin Li / Jinyue Wang / Xin Mao / Fei Shao / Youchun Wang / Ravindra Kumar Gupta / Yunlong Cao / Xiangxi Wang /
Abstract: Selective pressures have given rise to a number of SARS-CoV-2 variants during the prolonged course of the COVID-19 pandemic. Recently evolved variants differ from ancestors in additional ...Selective pressures have given rise to a number of SARS-CoV-2 variants during the prolonged course of the COVID-19 pandemic. Recently evolved variants differ from ancestors in additional glycosylation within the spike protein receptor-binding domain (RBD). Details of how the acquisition of glycosylation impacts viral fitness and human adaptation are not clearly understood. Here, we dissected the role of N354-linked glycosylation, acquired by BA.2.86 sub-lineages, as a RBD conformational control element in attenuating viral infectivity. The reduced infectivity is recovered in the presence of heparin sulfate, which targets the 'N354 pocket' to ease restrictions of conformational transition resulting in a 'RBD-up' state, thereby conferring an adjustable infectivity. Furthermore, N354 glycosylation improved spike cleavage and cell-cell fusion, and in particular escaped one subset of ADCC antibodies. Together with reduced immunogenicity in hybrid immunity background, these indicate a single spike amino acid glycosylation event provides selective advantage in humans through multiple mechanisms.
History
DepositionJan 15, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38701.png

Downloads & links

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Map

FileDownload / File: emd_38701.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 128 pix.
= 240.64 Å		1.88 Å/pix.
x 128 pix.
= 240.64 Å		1.88 Å/pix.
x 128 pix.
= 240.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.111
CCP4 map header1.881.881.88
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.399
Minimum - Maximum-0.4028984 - 1.7000835
Average (Standard dev.)0.0024960604 (±0.049711496)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38701_half_map_1.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 : XBB.1.5-K356T S-trimer (3 RBDs down)

EntireName: XBB.1.5-K356T S-trimer (3 RBDs down)
Components
  • Complex: XBB.1.5-K356T S-trimer (3 RBDs down)

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Supramolecule #1: XBB.1.5-K356T S-trimer (3 RBDs down)

SupramoleculeName: XBB.1.5-K356T S-trimer (3 RBDs down) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57082
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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