8X7X

Crystal structure of SADS-CoV fusion core

  • Classification: VIRAL PROTEIN
  • Organism(s): Coronaviridae
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-11-26 Released: 2024-02-21 
  • Deposition Author(s): Yan, L.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Fusion Cores from CCoV-HuPn-2018 and SADS-CoV.

Wang, F.Yang, G.Yan, L.

(2024) Viruses 16

  • DOI: https://doi.org/10.3390/v16020272
  • Primary Citation of Related Structures:  
    8X7X, 8X7Z

  • PubMed Abstract: 

    Cross-species spillover to humans of coronaviruses (CoVs) from wildlife animal reservoirs poses marked and global threats to human and animal health. Recently, sporadic infection of canine coronavirus-human pneumonia-2018 (CCoV-HuPn-2018) in hospitalized patients with pneumonia genetically related to canine and feline coronavirus were identified. In addition, swine acute diarrhea syndrome coronavirus (SADS-CoV) had the capability of broad tropism to cultured cells including from humans. Together, the transmission of Alphacoronaviruses that originated in wildlife to humans via intermediate hosts was responsible for the high-impact emerging zoonosis. Entry of CoV is mainly mediated by Spike and formation of a typical six helix bundle (6-HB) structure in the postfusion state of Spike is pivotal. Here, we present the complete fusion core structures of CCoV-HuPn-2018 and SADS-CoV from Alphacoronavirus at 2.10 and 2.59 Å, respectively. The overall structure of the CCoV-HuPn-2018 fusion core is similar to Alphacoronavirus like HCoV-229E, while SADS-CoV is analogous to Betacoronavirus like SARS-CoV-2. Collectively, we provide a structural basis for the development of pan-CoV small molecules and polypeptides based on the HR1-HR2 complex, concerning CCoV-HuPn-2018 and SADS-CoV.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HR1A [auth C]76CoronaviridaeMutation(s): 0 
UniProt
Find proteins for A8JNZ2 (Rhinolophus bat coronavirus HKU2)
Explore A8JNZ2 
Go to UniProtKB:  A8JNZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8JNZ2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HR2B [auth F]36CoronaviridaeMutation(s): 0 
UniProt
Find proteins for A8JNZ2 (Rhinolophus bat coronavirus HKU2)
Explore A8JNZ2 
Go to UniProtKB:  A8JNZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8JNZ2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.176α = 90
b = 45.176β = 90
c = 418.012γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-02-21 
  • Deposition Author(s): Yan, L.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Derived calculations
  • Version 1.2: 2024-03-13
    Changes: Database references