Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation

Ekal L Wendscheck D, David Y, Chojnowski G, Jeffries C, Mullapudi E, Schuldiner M, Warscheid B, Zalckvar E, Wilmanns M, (2025) DOI

SASDXC4 – Peroxisomal biogenesis factor 8 (Pex8) bound to the C-terminal domain of Peroxisomal targeting signal receptor, Pex5 (Pex8-Pex5CTD complex from P. pastoris)

Peroxisomal biogenesis factor 8
Peroxisomal targeting signal receptor
MWexperimental 101 kDa
MWexpected 114 kDa
VPorod 141 nm3
log I(s) 3.57×10-2 3.57×10-3 3.57×10-4 3.57×10-5
Peroxisomal biogenesis factor 8 Peroxisomal targeting signal receptor small angle scattering data  s, nm-1
ln I(s)
Peroxisomal biogenesis factor 8 Peroxisomal targeting signal receptor Guinier plot ln 3.57×10-2 Rg: 4.2 nm 0 (4.2 nm)-2 s2
(sRg)2I(s)/I(0)
Peroxisomal biogenesis factor 8 Peroxisomal targeting signal receptor Kratky plot 1.104 0 3 sRg
p(r)
Peroxisomal biogenesis factor 8 Peroxisomal targeting signal receptor pair distance distribution function Rg: 4.3 nm 0 Dmax: 14.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Peroxisomal biogenesis factor 8 Peroxisomal targeting signal receptor OTHER [STATIC IMAGE] model
Peroxisomal biogenesis factor 8 Peroxisomal targeting signal receptor SASREF model

Synchrotron SAXS data from solutions of the Pex8-Pex5CTD complex in 50 mM HEPES, 150 mM NaCl, 3% v/v glycerol, pH 7.5 were collected on the EMBL P12 beam line at PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123982 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 90.00 μl sample at 5.8 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 63 successive 0.500 second frames were collected through the main SEC elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The experimental molecular weight was estimated using Bayesian inference in the MW rage of 92-107 kDa (datmw tool, ATSAS 3; GNOM.out file input). SASREF models and the unsubtracted SEC-SAXS data frames are made available in the full entry zip archive.

Peroxisomal biogenesis factor 8 (Pex8)
Mol. type   Protein
Organism   Komagataella pastoris
Olig. state   Monomer
Mon. MW   78.0 kDa
 
UniProt   Q01962 (33-713)
Sequence   FASTA
 
Peroxisomal targeting signal receptor (Pex5)
Mol. type   Protein
Organism   Komagataella pastoris
Olig. state   Monomer
Mon. MW   36.1 kDa
 
UniProt   P33292 (259-576)
Sequence   FASTA