9FH0 | pdb_00009fh0

Pex5-Eci1 complex - Pex5 local refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A cryo-electron microscopy structure of yeast Pex5 in complex with a cargo uncovers a novel binding interface.

Peer, L.Dym, O.Elad, N.Tirosh, A.Jacobovitch, J.Sivan, E.Angel, M.Albeck, S.Schuldiner, M.Peleg, Y.Zalckvar, E.

(2025) J Cell Sci 138

  • DOI: https://doi.org/10.1242/jcs.263890
  • Primary Citation of Related Structures:  
    9FGZ, 9FH0

  • PubMed Abstract: 

    Proper protein targeting to organelles is crucial for maintaining eukaryotic cellular function and homeostasis. This necessity has driven the evolution of specific targeting signals on proteins and the targeting factors that recognize them. A prominent example is peroxisomal matrix proteins, most of which depend on the targeting factor Pex5 to localize and function correctly. Although most Pex5 cargoes contain a peroxisomal targeting signal type 1 (PTS1), they are not all targeted similarly. Some undergo priority targeting, facilitated either by stronger binding to specific subsets of PTS1 signals or by additional interaction interfaces. These observations highlight the extensive complexity of Pex5-mediated targeting. In this study, we reveal that the Saccharomyces cerevisiae (yeast) matrix protein Eci1 can reach peroxisomes and bind Pex5 in the absence of PTS1. By solving the structure of the yeast Pex5-Eci1 complex using cryo-electron microscopy, we identified additional binding interfaces. Our findings provide new insights into the versatile interactions between Pex5 and its cargo, Eci1. More broadly, this work highlights the intricate, dynamic nature of the interactions between cargo factors and their cargoes to meet the complex environment within eukaryotic cells.


  • Organizational Affiliation
    • Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3,2-trans-enoyl-CoA isomerase280Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ECI1
EC: 5.3.3.8
UniProt
Find proteins for Q05871 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05871 
Go to UniProtKB:  Q05871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05871
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisomal targeting signal receptorB [auth G]612Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PEX5PAS10YDR244WYD8419.11
UniProt
Find proteins for P35056 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35056 
Go to UniProtKB:  P35056
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35056
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.15.2_3472:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union864068
Israel Science FoundationIsrael760/17

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references