9FEE | pdb_00009fee

Cryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb9FEE/pdb
• EM Map EMD-50339: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• 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: 3.03 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: Dihedral - D2  (Explore in 3D)
Global 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: 140.55 kDa 
• Atom Count: 9,112 
• Modeled Residue Count: 1,236 
• Deposited Residue Count: 1,324 
• Unique protein chains: 1

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 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