8XZ4 | pdb_00008xz4

SARS-CoV-2 S and radixin complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.266 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8XZ4

This is version 1.1 of the entry. See complete history

Literature

SARS-CoV-2 S assembly into virions facilitated by host ERM proteins.

Wang, J.Tai, W.Wang, Z.Dai, W.Yang, M.Guo, J.He, P.Nan, Y.Li, T.Zhou, S.Cui, D.Li, Y.Ma, C.Zhang, Y.Li, D.Zhu, Z.Chu, K.Wang, D.Yang, S.Zhuang, X.Tian, M.Huang, M.Zhang, X.Cheng, G.Ma, W.

(2026) Proc Natl Acad Sci U S A 123: e2504517123-e2504517123

  • DOI: https://doi.org/10.1073/pnas.2504517123
  • Primary Citation Related Structures: 
    8XZ0, 8XZ4, 8XZ5, 8XZ6

  • PubMed Abstract: 

    The host cell cytoskeleton plays a critical role in the SARS-CoV-2 life cycle, though the underlying mechanisms remain poorly understood. This study investigates the interaction between the SARS-CoV-2 spike (S) protein and the cytoskeleton-associated ezrin-radixin-moesin (ERM) proteins through biochemical and structural characterization. A previously unidentified ERM-binding motif on the SARS-CoV-2 S protein is identified, revealing that S-ERM interactions are specifically conserved among highly pathogenic coronaviruses, including SARS-CoV, MERS-CoV, and SARS-CoV-2. Functionally, these interactions facilitate S packaging into virions by directing it to assembly sites, utilizing ERM's affinity for negatively curved membranes, akin to its role in cell surface protrusions. Silencing ERM expression significantly reduces SARS-CoV-2 titer, highlighting its essential role in viral propagation. Additionally, leveraging the established role of COPI-mediated trafficking in S localization, a compound is developed to disrupt S-COPI binding, promoting S secretion to the cell surface and effectively reducing viral titers. Our findings revealed a critical host-pathogen interaction that drives S incorporation into virions and identified ERM proteins as key facilitators of coronavirus assembly. Furthermore, our study suggests an antiviral strategy by targeting the S-COPI trafficking pathway. These insights advanced our understanding of coronavirus-host interactions and provided a potential therapeutic approach against SARS-CoV-2 and other highly pathogenic coronaviruses.


  • Organizational Affiliation
    • School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China.

Macromolecule Content 

  • Total Structure Weight: 36.77 kDa 
  • Atom Count: 2,634 
  • Modeled Residue Count: 306 
  • Deposited Residue Count: 310 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Radixin296Homo sapiensMutation(s): 0 
Gene Names: RDX
UniProt & NIH Common Fund Data Resources
Find proteins for P35241 (Homo sapiens)
Explore P35241 
Go to UniProtKB:  P35241
PHAROS:  P35241
GTEx:  ENSG00000137710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35241
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S2'14Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.266 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.375α = 90
b = 77.375β = 90
c = 58.444γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references