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- EMDB-39817: Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion inte... -

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Entry
Database: EMDB / ID: EMD-39817
TitleCryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of S2-bottom)
Map data
Sample
  • Complex: SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused on S2-bottom)
KeywordsSpike-ACE2 complex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsLiu Z / Xing L
Funding support China, 7 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2302500 China
National Natural Science Foundation of China (NSFC)82394463; 92169112; 82341036 China
National Key R&D Program of China2022YFC2604100; 2021YFC2300703; 2023YFC2307800 China
Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences2023-PT310-02 China
Major Project of Guangzhou National LaboratoryGZNL2023A01008; GZNL2024A01008 China
R&D Program of Guangzhou LaboratorySRPG22-003 China
Shanghai Municipal Science and Technology Major ProjectZD2021CY001 China
CitationJournal: Cell / Year: 2025
Title: Early fusion intermediate of ACE2-using coronavirus spike acting as an antiviral target.
Authors: Lixiao Xing / Zhimin Liu / Xinling Wang / Qianying Liu / Wei Xu / Qiyu Mao / Xiang Zhang / Aihua Hao / Shuai Xia / Zezhong Liu / Lujia Sun / Guangxu Zhang / Qian Wang / Zhenguo Chen / Shibo ...Authors: Lixiao Xing / Zhimin Liu / Xinling Wang / Qianying Liu / Wei Xu / Qiyu Mao / Xiang Zhang / Aihua Hao / Shuai Xia / Zezhong Liu / Lujia Sun / Guangxu Zhang / Qian Wang / Zhenguo Chen / Shibo Jiang / Lei Sun / Lu Lu /
Abstract: Coronavirus fusion with and entry into the host cell depends on viral spike, which acts as a crucial component of viral infection. However, the lack of receptor-activated spike intermediate ...Coronavirus fusion with and entry into the host cell depends on viral spike, which acts as a crucial component of viral infection. However, the lack of receptor-activated spike intermediate conformation has hindered a comprehensive understanding of spike-induced membrane fusion. Here, we captured an angiotensin-converting enzyme 2 (ACE2)-induced early fusion intermediate conformation (E-FIC) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike in which heptad repeat 1 (HR1) in S2 has ejected while S1 remains attached. This E-FIC can transition to the late FIC after S2' cleavage. Leveraging this discovery, we designed an E-FIC-targeted dual-functional antiviral protein, AL5E. AL5E effectively inactivated ACE2-using coronaviruses and inhibited their infection, outperforming a mono-functional antiviral in protecting animals against these coronaviruses. This study has identified the E-FIC and used it as a target for the development of a dual-functional antiviral for the prevention and treatment of ACE2-using coronavirus infection.
History
DepositionApr 20, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39817.png

Downloads & links

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Map

FileDownload / File: emd_39817.map.gz / Format: CCP4 / Size: 244.1 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.)
0.93 Å/pix.
x 400 pix.
= 372.8 Å		0.93 Å/pix.
x 400 pix.
= 372.8 Å		0.93 Å/pix.
x 400 pix.
= 372.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.13975887 - 16.70158
Average (Standard dev.)-0.05155194 (±0.23589447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39817_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_39817_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 S trimer in the early fusion intermediate conformation...

EntireName: SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused on S2-bottom)
Components
  • Complex: SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused on S2-bottom)

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Supramolecule #1: SARS-CoV-2 S trimer in the early fusion intermediate conformation...

SupramoleculeName: SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused on S2-bottom)
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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69402
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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