8OS1

X-ray structure of the Peroxisomal Targeting Signal 1 (PTS1) of Trypanosoma Cruzi PEX5 in complex with the PTS1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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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 : 135510-135510

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.135510
  • Primary Citation of Related Structures:  
    8OS1, 9F8W

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome targeting signal 1 receptorA [auth B],
B [auth A]
323Trypanosoma cruziMutation(s): 0 
Gene Names: ECC02_006719
UniProt
Find proteins for A0A7J6Y110 (Trypanosoma cruzi)
Explore A0A7J6Y110 
Go to UniProtKB:  A0A7J6Y110
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7J6Y110
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisomal targeting signal 1 (PTS1)C [auth D],
D [auth C]
5Trypanosoma cruziMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
U [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
I [auth B],
R [auth A],
T [auth A]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth B]
G [auth B]
H [auth B]
K [auth B]
L [auth B]
E [auth B],
G [auth B],
H [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth A],
P [auth A],
Q [auth A],
S [auth A],
V [auth A],
W [auth A],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.331α = 90
b = 69.936β = 100.05
c = 71.106γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
AutoProcessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Accelerated Early staGe drug dIScovery (AEGIS)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release