8Z7B | pdb_00008z7b

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2)

  • Classification: VIRAL PROTEIN
  • Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2024-04-19 Released: 2025-02-05 
  • Deposition Author(s): Liu, Z., Xing, L.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC), National Key R&D Program of China, Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences, Major Project of Guangzhou National Laboratory, R&D Program of Guangzhou Laboratory, Shanghai Municipal Science and Technology Major Project

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Early fusion intermediate of ACE2-using coronavirus spike acting as an antiviral target.

Xing, L.Liu, Z.Wang, X.Liu, Q.Xu, W.Mao, Q.Zhang, X.Hao, A.Xia, S.Liu, Z.Sun, L.Zhang, G.Wang, Q.Chen, Z.Jiang, S.Sun, L.Lu, L.

(2025) Cell 188: 1297-1314.e24

  • DOI: https://doi.org/10.1016/j.cell.2025.01.012
  • Primary Citation of Related Structures:  
    8Z3W, 8Z4X, 8Z64, 8Z6A, 8Z7B, 8Z7G, 8Z7L, 8Z7P

  • PubMed 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 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.


  • Organizational Affiliation
    • Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Shanghai Medical College, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai 200032, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2A [auth D]631Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Glycosylation
Glycosylation Sites: 6Go to GlyGen: Q9BYF1-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinB [auth C],
C [auth A]
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 7Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D [auth B],
E,
F,
G,
H,
D [auth B],
E,
F,
G,
H,
I,
J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFC2302500
National Natural Science Foundation of China (NSFC)China82394463; 92169112; 82341036
National Key R&D Program of ChinaChina2022YFC2604100; 2021YFC2300703; 2023YFC2307800
Non-profit Central Research Institute Fund of Chinese Academy of Medical SciencesChina2023-PT310-02
Major Project of Guangzhou National LaboratoryChinaGZNL2023A01008; GZNL2024A01008
R&D Program of Guangzhou LaboratoryChinaSRPG22-003
Shanghai Municipal Science and Technology Major ProjectChinaZD2021CY001

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection
  • Version 1.2: 2025-07-23
    Changes: Data collection, Database references