8GI0

Structure of Trypanosoma docking complex

• PDB DOI: https://doi.org/10.2210/pdb8GI0/pdb
• EM Map EMD-40056: EMDB EMDataResource

• Classification: PROTEIN TRANSPORT
• Organism(s): Trypanosoma cruzi, Trypanosoma cruzi strain CL Brener, Trypanosoma cruzi cruzi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-13 Released: 2024-03-27 
• Deposition Author(s): Sonani, R.R., Artur, B., Jemiola-Rzeminska, M., Lipinski, O., 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: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Noncanonical interactions and conformational dynamics in cargo-Pex5-Pex14 ternary complex for peroxisomal import

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

(2023) bioRxiv 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 251.2 kDa 
• Atom Count: 12,189 
• Modelled Residue Count: 1,625 
• Deposited Residue Count: 2,330 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal membrane protein PEX14	A [auth F]	372	Trypanosoma cruzi	Mutation(s): 0  Gene Names: C3747_80g13
UniProt
Find proteins for A0A2V2WKZ5 (Trypanosoma cruzi) Explore A0A2V2WKZ5  Go to UniProtKB:  A0A2V2WKZ5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
malate dehydrogenase	B [auth A], C [auth B], D [auth C], E [auth D]	323	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: Tc00.1047053506503.69
UniProt
Find proteins for Q4DRD8 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DRD8  Go to UniProtKB:  Q4DRD8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome targeting signal 1 receptor	F [auth E]	666	Trypanosoma cruzi cruzi	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: 3.50 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: 2024-03-27 
Deposition Author(s): Sonani, R.R., Artur, B., Jemiola-Rzeminska, M., Lipinski, O., 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

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Structure summary