Selective cargo and membrane recognition by SNX17 regulates its interaction with Retriever

Martín-González A, Méndez-Guzmán I, Zabala-Zearreta M, Quintanilla A, García-López A, Martínez-Lombardía E, Albesa-Jové D, Acosta J, Lucas M, EMBO Reports (2024) DOI

SASDVQ6 – Retriever complex

VPS35 endosomal protein-sorting factor-like
Vacuolar protein sorting-associated protein 29
Vacuolar protein sorting-associated protein 26C
MWexperimental 170 kDa
MWexpected 163 kDa
VPorod 256 nm3
log I(s) 1.28×10-1 1.28×10-2 1.28×10-3 1.28×10-4
VPS35 endosomal protein-sorting factor-like Vacuolar protein sorting-associated protein 29 Vacuolar protein sorting-associated protein 26C small angle scattering data  s, nm-1
ln I(s)
VPS35 endosomal protein-sorting factor-like Vacuolar protein sorting-associated protein 29 Vacuolar protein sorting-associated protein 26C Guinier plot ln 1.28×10-1 Rg: 5.2 nm 0 (5.2 nm)-2 s2
(sRg)2I(s)/I(0)
VPS35 endosomal protein-sorting factor-like Vacuolar protein sorting-associated protein 29 Vacuolar protein sorting-associated protein 26C Kratky plot 1.104 0 √3 sRg
p(r)
VPS35 endosomal protein-sorting factor-like Vacuolar protein sorting-associated protein 29 Vacuolar protein sorting-associated protein 26C pair distance distribution function Rg: 5.4 nm 0 Dmax: 21.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
VPS35 endosomal protein-sorting factor-like Vacuolar protein sorting-associated protein 29 Vacuolar protein sorting-associated protein 26C ALPHAFOLD model
log I(s)
 s, nm-1
VPS35 endosomal protein-sorting factor-like Vacuolar protein sorting-associated protein 29 Vacuolar protein sorting-associated protein 26C ALPHAFOLD model
log I(s)
 s, nm-1
VPS35 endosomal protein-sorting factor-like Vacuolar protein sorting-associated protein 29 Vacuolar protein sorting-associated protein 26C GASBOR model
Synchrotron SAXS data from solutions of the Retriever complex in 50 mM Tris, 200 mM NaCl, 1 mM TCEP, pH 7.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.0954 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 45.00 μl sample at 5 mg/ml was injected at a 0.16 ml/min flow rate onto a Shodex KW403-4F column at 15°C. 600 successive 3 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

VPS35 endosomal protein-sorting factor-like (VPS35L)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   109.6 kDa
 
UniProt   Q7Z3J2 (1-963)
Sequence   FASTA
 
Vacuolar protein sorting-associated protein 29 (VPS29)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   20.5 kDa
 
UniProt   Q9UBQ0 (1-182)
Sequence   FASTA
 
Vacuolar protein sorting-associated protein 26C (VPS26C)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   33.1 kDa
 
UniProt   O14972 (1-297)
Sequence   FASTA