8X4N | pdb_00008x4n

Crystal structure of the PI3P-binding domain of Legionella SetA in complex with inositol 1,3-bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.253 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into SetA-mediated Rab1 glucosylation and PI3P-guided localization during early Legionella infection.

Im, H.N.Lee, Y.Song, Y.Hahn, H.Jeon, H.Shin, D.Lee, S.Kim, K.H.Kim, K.T.Suh, S.W.Jang, D.M.Kim, H.S.

(2026) Proc Natl Acad Sci U S A 123: e2535016123-e2535016123

  • DOI: https://doi.org/10.1073/pnas.2535016123
  • Primary Citation Related Structures: 
    8X4J, 8X4K, 8X4M, 8X4N

  • PubMed Abstract: 

    The bacterial pathogen Legionella pneumophila secretes effector proteins that remodel host endomembranes to establish a replication-permissive niche known as the Legionella -containing vacuole (LCV). Among these, SetA disrupts vesicle trafficking by glucosylating the small GTPase Rab1, essential for ER-to-Golgi transport. Here, we report comprehensive structural and mechanistic insights into SetA-mediated Rab1 glucosylation and its PI3P-dependent membrane targeting. Crystal structures of its N-terminal glycosyltransferase and C-terminal lipid-binding domains, captured in multiple ligand-bound states, reveal how SetA specifically recognizes GDP-bound Rab1 and the head group of phosphatidylinositol 3-phosphate (PI3P), which is enriched on early LCV membranes. SAXS-based full-length modeling, biochemical assays, and cellular imaging analyses demonstrate that SetA integrates Rab1 modification with membrane localization, thereby perturbing Golgi integrity and ER morphology. Together, these findings define the dual structural mechanisms underlying SetA's coordination of substrate glucosylation and membrane association, providing a spatiotemporal framework for understanding Legionella 's early infection strategy.


  • Organizational Affiliation
    • Research Institute, National Cancer Center, Goyang 10408, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subversion of eukaryotic traffic protein A
A, B
126Legionella pneumophilaMutation(s): 0 
Gene Names: setA
EC: 2.4.1
UniProt
Find proteins for Q5ZU30 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZU30 
Go to UniProtKB:  Q5ZU30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZU30
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.253 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.247α = 90
b = 36.915β = 111.61
c = 72.407γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2026-04-08
    Changes: Database references