5OSI

Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.205 

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 Legionella pneumophila encodes RidL to hijack the host scaffold protein VPS29, a component of retromer and retriever complexes cri ...

    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

    Structural Biology Unit, Centro de Investigación Cooperativa en Biociencias, 48160 Derio, 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
311Homo 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
14Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Mutation(s): 0 
Find proteins for Q5ZT54 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Go to UniProtKB:  Q5ZT54
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
E, H, K
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, D, G, H, J, K
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.554α = 90.00
b = 138.993β = 92.78
c = 126.637γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
xia2data scaling
XDSdata reduction

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: 2019-01-09
    Type: Data collection, Structure summary