9I4X | pdb_00009i4x

Toxoplasma gondii cytochrome bc1 complex from the respiratory supercomplex III2-IV inhibited by atovaquone and ELQ-300


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 32: 1424-1433

  • 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bA,
M [auth a]
368Toxoplasma gondii GT1Mutation(s): 1 
Gene Names: MT-CYBCOBCYTBMTCYB
UniProt
Find proteins for O20672 (Toxoplasma gondii)
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UniProt GroupO20672
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme proteinB,
N [auth b]
398Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_246540
UniProt
Find proteins for S7W9J5 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupS7W9J5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ubiquinol cytochrome c oxidoreductaseC,
O [auth c]
487Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_320220
EC: 1.10.2.2
UniProt
Find proteins for S7UK06 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupS7UK06
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Putative peptidase M16 family poteinD,
P [auth d]
509Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_236210
EC: 3.4.24.64
UniProt
Find proteins for S7W617 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupS7W617
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-MPPE,
Q [auth e]
563Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_202680
EC: 3.4.24.64
UniProt
Find proteins for A0A125YN38 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupA0A125YN38
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ubiquinol-cytochrome c reductase hinge proteinF,
R [auth f]
89Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_320140
UniProt
Find proteins for S7VSS5 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupS7VSS5
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductaseG,
S [auth g]
234Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_288750
UniProt
Find proteins for A0A125YYJ3 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupA0A125YYJ3
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
QCR8, TGGT1_227910H,
T [auth h]
122Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_227910
UniProt
Find proteins for A0A125YW19 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C family reductase UQCRX/QCR9-like proteinI,
U [auth i]
128Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_201880
UniProt
Find proteins for S7UVH4 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupS7UVH4
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinJ,
V [auth j]
80Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_214250
UniProt
Find proteins for S7UR33 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinK,
W [auth k]
141Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_207170
UniProt
Find proteins for A0A125YZN9 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupA0A125YZN9
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinL,
X [auth l]
109Toxoplasma gondii GT1Mutation(s): 0 
Gene Names: TGGT1_312940
UniProt
Find proteins for S7UTB5 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
CB [auth d]
EA [auth B]
EB [auth g]
FB [auth l]
IA [auth C]
CB [auth d],
EA [auth B],
EB [auth g],
FB [auth l],
IA [auth C],
KA [auth D],
MA [auth G],
NA [auth I],
OA [auth J],
PA [auth L],
QA [auth a],
WA [auth b],
Y [auth A],
YA [auth c]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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BB [auth c],
HA [auth C],
JA [auth C],
ZA [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

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FA [auth B],
XA [auth b]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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CA [auth A],
DA [auth A],
UA [auth a],
VA [auth a]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1IJD (Subject of Investigation/LOI)
Query on A1IJD

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AA [auth A],
BA [auth A],
SA [auth a],
TA [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
AOQ (Subject of Investigation/LOI)
Query on AOQ

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RA [auth a],
Z [auth A]
2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione
C22 H19 Cl O3
KUCQYCKVKVOKAY-CTYIDZIISA-N
FES
Query on FES

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AB [auth c],
GA [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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DB [auth d],
LA [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references