9I5R | pdb_00009i5r

Interactions between Pex3 and Pex19 peptide in yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 
    0.248 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Competition between binding partners of yeast Pex3 affects peroxisome biology.

de Lange, E.M.F.Chojnowski, G.Burgi, J.Vlijm, R.Wilmanns, M.van der Klei, I.J.

(2025) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70229
  • Primary Citation of Related Structures:  
    9I5R

  • PubMed Abstract: 

    Peroxisomes are important membrane-bound organelles that are involved in a multitude of metabolic processes. Peroxisomal biogenesis factor 3 (Pex3) is a crucial peroxisomal membrane protein (PMP) that plays a vital role in many of these processes through the specific recruitment of several binding partners. In the yeast Hansenula polymorpha, Pex3 recruits PMP import receptor Pex19, the receptor for newly synthesized PMPs; autophagy-related protein 30 (Atg30), a protein involved in the selective breakdown of peroxisomes (pexophagy); and inheritance of peroxisomes protein 1 (Inp1), a protein important for peroxisome retention in mother cells. Here, we show that the overexpression of any of these proteins affects peroxisomal processes, with the level of overexpression being the primary determinant of competition. This finding is confirmed by our analysis based on the crystal structure model of the H. polymorpha Pex3-Pex19 complex and AlphaFold2 predictions. It shows that the interaction regions of Pex3 with these proteins overlap. These results provide a crucial insight into the complex role of Pex3 in regulating different processes in peroxisome biology.


  • Organizational Affiliation
    • Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisomal biogenesis factor 3421Ogataea angustaMutation(s): 0 
Gene Names: PEX3PER9
UniProt
Find proteins for Q01497 (Pichia angusta)
Explore Q01497 
Go to UniProtKB:  Q01497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01497
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxin19 Pex19p23Ogataea angustaMutation(s): 0 
Gene Names: PEX19
UniProt
Find proteins for Q96WN7 (Pichia angusta)
Explore Q96WN7 
Go to UniProtKB:  Q96WN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96WN7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.579α = 90
b = 137.224β = 90
c = 111.534γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Database references