7U2V | pdb_00007u2v

Plasmodium falciparum Cyt c2 DSD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.243 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1073/pnas.2301047120
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c2
A, B
159Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1311700
UniProt
Find proteins for Q8I6T6 (Plasmodium falciparum (isolate 3D7))
Explore Q8I6T6 
Go to UniProtKB:  Q8I6T6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I6T6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.846α = 90
b = 54.613β = 102.19
c = 71.464γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
SOLVEphasing
RESOLVEmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HECClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133764

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary