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 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1073/pnas.1715361115
  • Primary Citation of Related Structures:  
    5OSH, 5OSI, 5OT4

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 29
A, D, G, J
182Homo sapiensMutation(s): 0 
Gene Names: VPS29DC15DC7MDS007
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBQ0 (Homo sapiens)
Explore Q9UBQ0 
Go to UniProtKB:  Q9UBQ0
PHAROS:  Q9UBQ0
GTEx:  ENSG00000111237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBQ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 35
B, E, H, K
311Homo sapiensMutation(s): 0 
Gene Names: VPS35MEM3TCCCTA00141
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QK1 (Homo sapiens)
Explore Q96QK1 
Go to UniProtKB:  Q96QK1
PHAROS:  Q96QK1
GTEx:  ENSG00000069329 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QK1
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interaptin
C, F, I
14Legionella pneumophila subsp. pneumophila ATCC 43290Mutation(s): 0 
Gene Names: lp12_2303
UniProt
Find proteins for Q5ZT54 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZT54 
Go to UniProtKB:  Q5ZT54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZT54
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
L [auth A]
M [auth B]
N [auth D]
O [auth D]
Q [auth G]
L [auth A],
M [auth B],
N [auth D],
O [auth D],
Q [auth G],
R [auth H],
T [auth J],
U [auth J],
V [auth K],
W [auth K],
X [auth K]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
P [auth E],
S [auth H],
Y [auth K],
Z [auth K]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.554α = 90
b = 138.993β = 92.78
c = 126.637γ = 90
Software Package:
Software NamePurpose
xia2data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2018-01-03
    Changes: Database references
  • Version 1.3: 2019-01-09
    Changes: Data collection, Structure summary
  • Version 1.4: 2024-01-17
    Changes: Author supporting evidence, Data collection, Database references, Refinement description