7TXE | pdb_00007txe

Plasmodium falciparum Cyt c2 DSD

• PDB DOI: https://doi.org/10.2210/pdb7TXE/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-02-08 Released: 2023-05-10 
• Deposition Author(s): Hill, C.P., Wienkers, H.J., Whitby, F.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasites

Espino-Sanchez, T.J., Wienkers, H., Marvin, R.G., Nalder, S.A., Garcia-Guerrero, A.E., VanNatta, P.E., Jami-Alahmadi, Y., Mixon Blackwell, A., Whitby, F.G., Wohlschlegel, J.A., Kieber-Emmons, M.T., Hill, C.P., Sigala, P.A.

(2023) Proc Natl Acad Sci U S A 120: e2301047120

• PubMed: 37126705 
• DOI: https://doi.org/10.1073/pnas.2301047120
• Primary Citation Related Structures: 
  7TXE, 7U2V


• PubMed Abstract: 
  

  The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs ( c and c -2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c -2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c ₁ for inducible knockdown. Translational repression of cyt c and cyt c ₁ was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c -2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c -2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c -2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.

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Organizational Affiliation: 
• Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112.
Department of Chemistry, University of Utah, Salt Lake City, UT 84112.
Department of Biological Chemistry, University of California, Los Angeles, CA 90095.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.22 kDa 
• Atom Count: 2,241 
• Modeled Residue Count: 262 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c2	A, B	159	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF3D7_1311700
UniProt
Find proteins for Q8I6T6 (Plasmodium falciparum (isolate 3D7)) Explore Q8I6T6  Go to UniProtKB:  Q8I6T6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A], D [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.44	α = 90
b = 71.994	β = 90
c = 78.409	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Hill, C.P., Wienkers, H.J., Whitby, F.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM133764

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Structure summary