9F8W | pdb_00009f8w

Crystal structure of the apo Pex5 peroxisomal cargo receptor from Trypanosoma brucei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.246 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structural dynamics of the TPR domain of the peroxisomal cargo receptor Pex5 in Trypanosoma.

Banasik, M.Napolitano, V.Blat, A.Abdulkarim, K.Plewka, J.Czaplewski, C.Gieldon, A.Kozak, M.Wladyka, B.Popowicz, G.Dubin, G.

(2024) Int J Biol Macromol 280: 135510-135510

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.135510

  • PubMed Abstract: 

    Peroxisomal protein import has been identified as a valid target in trypanosomiases, an important health threat in Central and South America. The importomer is built of multiple peroxins (Pex) and structural characterization of these proteins facilitates rational inhibitor development. We report crystal structures of the Trypanosoma brucei and T. cruzi tetratricopeptide repeat domain (TPR) of the cytoplasmic peroxisomal targeting signal 1 (PTS1) receptor Pex5. The structure of the TPR domain of TbPex5 represents an apo-form of the receptor which, together with the previously determined structure of the complex of TbPex5 TPR and PTS1 demonstrate significant receptor dynamics associated with signal peptide recognition. The structure of the complex of TPR domain of TcPex5 with PTS1 provided in this study details the molecular interactions that guide signal peptide recognition at the atomic level in the pathogenic species currently perceived as the most relevant among Trypanosoma. Small - angle X - ray scattering (SAXS) data obtained in solution supports the crystallographic findings on the compaction of the TPR domains of TbPex5 and TcPex5 upon interaction with the cargo.


  • Organizational Affiliation
    • Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.

Macromolecule Content 

  • Total Structure Weight: 77.84 kDa 
  • Atom Count: 4,949 
  • Modeled Residue Count: 632 
  • Deposited Residue Count: 694 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome targeting signal 1 receptor PEX5
A, B
347Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q57W55 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57W55 
Go to UniProtKB:  Q57W55
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57W55
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.545α = 90
b = 206.545β = 90
c = 67.867γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2017/26/M/NZ1/00797
Polish National Science CentrePoland2020/39/B/NZ1/01551

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary
  • Version 1.2: 2025-08-20
    Changes: Author supporting evidence