9FEF | pdb_00009fef

Cryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex

• PDB DOI: https://doi.org/10.2210/pdb9FEF/pdb
• EM Map EMD-50340: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Trypanosoma cruzi strain CL Brener
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-19 Released: 2024-05-29 
• Deposition Author(s): Lipinski, O., Sonani, R.R., Blat, A., Jemiola-Rzeminska, M., Patel, S.N., Sood, T., Dubin, G.
• Funding Organization(s): Polish National Science Centre, Foundation for Polish Science

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.98 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Trypanosoma peroxisomal import complex unveils conformational dynamics

Sonani, R.R., Blat, A., Jemiola-Rzeminska, M., Lipinski, O., Patel, S.N., Sood, T., Dubin, G.

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2023.04.03.535445

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy, light scattering

Macromolecule Content 

• Total Structure Weight: 215.85 kDa 
• Atom Count: 11,192 
• Modeled Residue Count: 1,502 
• Deposited Residue Count: 1,998 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
malate dehydrogenase	A, B, C, D	331	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: Tc00.1047053506503.69 EC: 1.1.1.37
UniProt
Find proteins for Q4DRD8 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DRD8  Go to UniProtKB:  Q4DRD8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome targeting signal 1 receptor	E	674	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: TCDM_08436
UniProt
Find proteins for V5B7T1 (Trypanosoma cruzi Dm28c) Explore V5B7T1  Go to UniProtKB:  V5B7T1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.98 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Lipinski, O., Sonani, R.R., Blat, A., Jemiola-Rzeminska, M., Patel, S.N., Sood, T., Dubin, G.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2017/26/M/NZ1/00797
Foundation for Polish Science	Poland	TEAM TECH CORE FACILITY/2017-4/6
Polish National Science Centre	Poland	2020/39/B/NZ1/01551

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2025-06-11
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-08-20
  Changes: Author supporting evidence, Data collection