5OSH

Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL.

Romano-Moreno, M.Rojas, A.L.Williamson, C.D.Gershlick, D.C.Lucas, M.Isupov, M.N.Bonifacino, J.S.Machner, M.P.Hierro, A.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E11151-E11160

  • DOI: 10.1073/pnas.1715361115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Microbial pathogens employ sophisticated virulence strategies to cause infections in humans. The intracellular pathogen <i>Legionella pneumophila </i> encodes RidL to hijack the host scaffold protein VPS29, a component of retromer and retriever comp ...

    Microbial pathogens employ sophisticated virulence strategies to cause infections in humans. The intracellular pathogen Legionella pneumophila encodes RidL to hijack the host scaffold protein VPS29, a component of retromer and retriever complexes critical for endosomal cargo recycling. Here, we determined the crystal structure of L. pneumophila RidL in complex with the human VPS29-VPS35 retromer subcomplex. A hairpin loop protruding from RidL inserts into a conserved pocket on VPS29 that is also used by cellular ligands, such as Tre-2/Bub2/Cdc16 domain family member 5 (TBC1D5) and VPS9-ankyrin repeat protein for VPS29 binding. Consistent with the idea of molecular mimicry in protein interactions, RidL outcompeted TBC1D5 for binding to VPS29. Furthermore, the interaction of RidL with retromer did not interfere with retromer dimerization but was essential for association of RidL with retromer-coated vacuolar and tubular endosomes. Our work thus provides structural and mechanistic evidence into how RidL is targeted to endosomal membranes.


    Organizational Affiliation

    The Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter EX4 4SB, United Kingdom.,Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; machnerm@mail.nih.gov ahierro@cicbiogune.es.,Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892.,Structural Biology Unit, Centro de Investigación Cooperativa en Biociencias, 48160 Derio, Spain.,Structural Biology Unit, Centro de Investigación Cooperativa en Biociencias, 48160 Derio, Spain; machnerm@mail.nih.gov ahierro@cicbiogune.es.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 29
A, D, G, J
182Homo sapiensMutation(s): 0 
Gene Names: VPS29
Find proteins for Q9UBQ0 (Homo sapiens)
Go to Gene View: VPS29
Go to UniProtKB:  Q9UBQ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 35
B, E, H, K
299Homo sapiensMutation(s): 0 
Gene Names: VPS35 (MEM3)
Find proteins for Q96QK1 (Homo sapiens)
Go to Gene View: VPS35
Go to UniProtKB:  Q96QK1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Interaptin
C, F, I, L
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.254 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.201α = 90.00
b = 173.243β = 90.00
c = 445.775γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-59759-R
Spanish Ministry of Economy and CompetitivenessSpainSEV-2016-0644
inextH2020 653706

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Database references
  • Version 1.2: 2018-01-03
    Type: Database references
  • Version 1.3: 2019-01-02
    Type: Data collection, Structure summary