7UPS

Structural study of Legionella pneumophila effector DotY (Lpg0294)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural study of Legionella pneumophila effector DotY (Lpg0294), a component of the Dot/Icm type IV secretion system.

Chung, I.Y.W.Cygler, M.

(2022) Acta Crystallogr F Struct Biol Commun 78: 276-280

  • DOI: https://doi.org/10.1107/S2053230X22006604
  • Primary Citation of Related Structures:  
    7UPS

  • PubMed Abstract: 

    The bacterium Legionella pneumophila is a causative agent of Legionnaires' disease. It utilizes the Dot/Icm type IV secretion system (T4SS) to deliver over 300 effector proteins into the host cell, leading to modification of cellular processes and creating a safe environment for bacterial proliferation. Dot/Icm is a multi-subunit molecular machine. The effectors are recognized by the inner membrane-embedded coupling complex (T4CC), which then delivers them to the translocation apparatus. This T4CC subcomplex is made up of DotL, DotM, DotN, IcmS, IcmW, LvgA, DotY and DotZ, and its structure was recently determined by cryo-EM. DotY is a highly mobile component of this subcomplex and its structure was only partially defined. DotY is a unique component of the T4SS that is only found in the Legionella genus. Here, the crystal structure of DotY on its own is presented and its fold and the connectivity of its secondary-structure elements are established. The protein is divided into three segments. The first and last segments form a four-helix bundle domain, while the middle segment forms an α/β domain that has a unique fold. The flexibility of the interdomain linkers allows the reorientation of the two domains between that observed in the crystal structure and that assumed within the T4CC subcomplex.


  • Organizational Affiliation

    Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DotY (Lpg0294)
A, B, C, D
215Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg0294
UniProt
Find proteins for Q5ZYR7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZYR7 
Go to UniProtKB:  Q5ZYR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZYR7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.2α = 90
b = 75.62β = 127.91
c = 101.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Data collection