8Z7G | pdb_00008z7g

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)

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

  • Deposited: 2024-04-20 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, R&D Program of Guangzhou LaboratoryShanghai Municipal Science and Technology Major Project

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)

Liu, Z., Xing, L.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: S, 2
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: 6
Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
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
R&D Program of Guangzhou LaboratoryShanghai Municipal Science and Technology Major ProjectChinaZD2021CY001

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release