7E0B

The crystal structure of sorting nexin 27 and PBM complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SNX27 suppresses SARS-CoV-2 infection by inhibiting viral lysosome/late endosome entry.

Yang, B.Jia, Y.Meng, Y.Xue, Y.Liu, K.Li, Y.Liu, S.Li, X.Cui, K.Shang, L.Cheng, T.Zhang, Z.Hou, Y.Yang, X.Yan, H.Duan, L.Tong, Z.Wu, C.Liu, Z.Gao, S.Zhuo, S.Huang, W.Gao, G.F.Qi, J.Shang, G.

(2022) Proc Natl Acad Sci U S A 119

  • DOI: https://doi.org/10.1073/pnas.2117576119
  • Primary Citation of Related Structures:  
    7E0B

  • PubMed Abstract: 

    After binding to its cell surface receptor angiotensin converting enzyme 2 (ACE2), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the host cell through directly fusing with plasma membrane (cell surface pathway) or undergoing endocytosis traveling to lysosome/late endosome for membrane fusion (endocytic pathway). However, the endocytic entry regulation by host cell remains elusive. Recent studies show ACE2 possesses a type I PDZ binding motif (PBM) through which it could interact with a PDZ domain-containing protein such as sorting nexin 27 (SNX27). In this study, we determined the ACE2-PBM/SNX27-PDZ complex structure, and, through a series of functional analyses, we found SNX27 plays an important role in regulating the homeostasis of ACE2 receptor. More importantly, we demonstrated SNX27, together with retromer complex (the core component of the endosomal protein sorting machinery), prevents ACE2/virus complex from entering lysosome/late endosome, resulting in decreased viral entry in cells where the endocytic pathway dominates. The ACE2/virus retrieval mediated by SNX27-retromer could be considered as a countermeasure against invasion of ACE2 receptor-using SARS coronaviruses.


  • Organizational Affiliation

    Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-2796Homo sapiensMutation(s): 0 
Gene Names: SNX27KIAA0488My014
UniProt & NIH Common Fund Data Resources
Find proteins for Q96L92 (Homo sapiens)
Explore Q96L92 
Go to UniProtKB:  Q96L92
PHAROS:  Q96L92
GTEx:  ENSG00000143376 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96L92
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PBM7Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.55α = 90
b = 88.55β = 90
c = 43.27γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description