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

SASDXB4 – Peroxisomal biogenesis factor 8 (Pex8) bound to the N-terminal domain of Peroxisomal targeting signal receptor, Pex5 (Pex8-Pex5NTD complex from P. pastoris)

Peroxisomal biogenesis factor 8
Peroxisomal targeting signal receptor
MWexperimental 119 kDa
MWexpected 110 kDa
VPorod 177 nm3
log I(s) 2.79×10-2 2.79×10-3 2.79×10-4 2.79×10-5
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 2.80×10-2 Rg: 4.6 nm 0 (4.6 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: 4.8 nm 0 Dmax: 19 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 CORAL model

Synchrotron SAXS data from solutions of the Pex8-Pex5NTD 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 (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 5.2 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 87 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 111-127 kDa (datmw tool, ATSAS 3; GNOM.out file input). CORAL 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   31.9 kDa
 
UniProt   P33292 (1-276)
Sequence   FASTA