9G9T | pdb_00009g9t

Cryo-EM structure of the Toxoplasma gondii respiratory chain complex III inhibited by ELQ-300


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex.

MacLean, A.E.Shikha, S.Ferreira Silva, M.Gramelspacher, M.J.Nilsen, A.Liebman, K.M.Pou, S.Winter, R.W.Meir, A.Riscoe, M.K.Doggett, J.S.Sheiner, L.Muhleip, A.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01531-7
  • Primary Citation of Related Structures:  
    9G9T, 9H8T, 9I4X

  • PubMed Abstract: 

    The apicomplexan mitochondrial electron transport chain is essential for parasite survival and displays a divergent subunit composition. Here we report cryo-electron microscopy structures of an apicomplexan III 2 -IV supercomplex and of the drug target complex III 2 . The supercomplex structure reveals how clade-specific subunits form an apicomplexan-conserved III 2 -IV interface with a unique, kinked architecture, suggesting that supercomplexes evolved independently in different eukaryotic lineages. A knockout resulting in supercomplex disassembly challenges the proposed role of III 2 -IV in electron transfer efficiency as suggested for mammals. Nevertheless, knockout analysis indicates that III 2 -IV is critical for parasite fitness. The complexes from the model parasite Toxoplasma gondii were inhibited with the antimalarial atovaquone, revealing interactions underpinning species specificity. They were also inhibited with endochin-like quinolone (ELQ)-300, an inhibitor in late-stage preclinical development. Notably, in the apicomplexan binding site, ELQ-300 is flipped compared with related compounds in the mammalian enzyme. On the basis of the binding modes and parasite-specific interactions discovered, we designed more potent ELQs with subnanomolar activity against T. gondii. Our findings reveal critical evolutionary differences in the role of supercomplexes in mitochondrial biology and provide insight into cytochrome b inhibition, informing future drug discovery.


  • Organizational Affiliation
    • School of Infection and Immunity, University of Glasgow, Glasgow, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bA,
M [auth a]
360Toxoplasma gondiiMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
UniProt
Find proteins for S8EQL3 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore S8EQL3 
Go to UniProtKB:  S8EQL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS8EQL3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme proteinB,
N [auth b]
398Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_246540
UniProt
Find proteins for A0A125YTU2 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YTU2 
Go to UniProtKB:  A0A125YTU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YTU2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ubiquinol cytochrome c oxidoreductaseC,
O [auth c]
487Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_320220
EC: 1.10.2.2
UniProt
Find proteins for A0A125YZC1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YZC1 
Go to UniProtKB:  A0A125YZC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YZC1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Putative peptidase M16 family proteinD,
P [auth d]
509Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_236210
EC: 3.4.24.64
UniProt
Find proteins for A0A125YS93 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YS93 
Go to UniProtKB:  A0A125YS93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YS93
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-MPPE,
Q [auth e]
563Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_202680
EC: 3.4.24.64
UniProt
Find proteins for S8GED8 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore S8GED8 
Go to UniProtKB:  S8GED8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS8GED8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ubiquinol-cytochrome c reductase hinge proteinF,
R [auth f]
89Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_320140
UniProt
Find proteins for A0A125YU99 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YU99 
Go to UniProtKB:  A0A125YU99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YU99
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductaseG,
S [auth g]
234Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_288750
UniProt
Find proteins for A0A125YYJ5 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YYJ5 
Go to UniProtKB:  A0A125YYJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YYJ5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
QCR8/TGGT1_227910H,
T [auth h]
122Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_227910
UniProt
Find proteins for A0A125YW21 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YW21 
Go to UniProtKB:  A0A125YW21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YW21
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C family reductase UQCRX/QCR9-like proteinI,
U [auth i]
128Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_201880
UniProt
Find proteins for A0A125YZ21 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YZ21 
Go to UniProtKB:  A0A125YZ21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YZ21
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinJ,
V [auth j]
80Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_214250
UniProt
Find proteins for A0A125YPC9 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YPC9 
Go to UniProtKB:  A0A125YPC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YPC9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinK,
W [auth k]
141Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_207170
UniProt
Find proteins for A0A125YZP0 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YZP0 
Go to UniProtKB:  A0A125YZP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YZP0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinL,
X [auth l]
109Toxoplasma gondiiMutation(s): 0 
Gene Names: TGGT1_312940
UniProt
Find proteins for A0A125YYV1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YYV1 
Go to UniProtKB:  A0A125YYV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YYV1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
AB [auth g]
BB [auth g]
CB [auth h]
GA [auth C]
HA [auth C]
AB [auth g],
BB [auth g],
CB [auth h],
GA [auth C],
HA [auth C],
IA [auth D],
KA [auth G],
LA [auth H],
MA [auth H],
NA [auth I],
OA [auth L],
PA [auth a],
WA [auth c],
XA [auth c],
Y [auth A],
YA [auth d]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

Download Ideal Coordinates CCD File 
DB [auth i],
FA [auth C]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
EA [auth B],
VA [auth b]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth A],
CA [auth A],
SA [auth a],
TA [auth a]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1IJD
Query on A1IJD

Download Ideal Coordinates CCD File 
AA [auth A],
QA [auth a],
RA [auth a],
Z [auth A]
6-chloranyl-7-methoxy-2-methyl-3-[4-[4-(trifluoromethyloxy)phenoxy]phenyl]-1~{H}-quinolin-4-one
C24 H17 Cl F3 N O4
WZDNKHCQIZRDKW-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JA [auth D],
ZA [auth d]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth A],
UA [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release