9H8T | pdb_00009h8t

Cryo-EM structure of the atovaquone-inhibited Complex III from the Chlorocebus sabaeus respirasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 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

  • 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 c1A [auth D],
L [auth d]
325Chlorocebus sabaeusMutation(s): 0 
UniProt
Find proteins for A0A0D9R8S7 (Chlorocebus sabaeus)
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UniProt GroupA0A0D9R8S7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialB [auth A],
K [auth T],
M [auth a]
274Chlorocebus sabaeusMutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for A0A0D9QXW2 (Chlorocebus sabaeus)
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UniProt GroupA0A0D9QXW2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7C [auth G],
N [auth g]
111Chlorocebus sabaeusMutation(s): 0 
UniProt
Find proteins for A0A0D9RJ49 (Chlorocebus sabaeus)
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UniProt GroupA0A0D9RJ49
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8D [auth C],
O [auth c]
82Chlorocebus sabaeusMutation(s): 0 
UniProt
Find proteins for A0A0D9RML3 (Chlorocebus sabaeus)
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UniProt GroupA0A0D9RML3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Complex III subunit 9E,
P [auth e]
63Chlorocebus sabaeusMutation(s): 0 
UniProt
Find proteins for A0A0D9RB67 (Chlorocebus sabaeus)
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UniProt GroupA0A0D9RB67
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6F,
Q [auth f]
91Chlorocebus sabaeusMutation(s): 0 
UniProt
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UniProt GroupA0A0D9S9I7
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase core protein 2G [auth K],
R [auth k]
453Chlorocebus sabaeusMutation(s): 0 
UniProt
Find proteins for A0A0D9R493 (Chlorocebus sabaeus)
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UniProt GroupA0A0D9R493
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bH [auth J],
S [auth j]
380Chlorocebus sabaeusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase core protein 1I [auth L],
T [auth l]
480Chlorocebus sabaeusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRBJ [auth H],
U [auth h]
56Chlorocebus sabaeusMutation(s): 0 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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GA [auth L],
LA [auth c],
TA [auth l],
Y [auth C]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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MA [auth e],
Z [auth E]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PEE
Query on PEE

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BA [auth J]
CA [auth J]
HA [auth L]
OA [auth j]
PA [auth j]
BA [auth J],
CA [auth J],
HA [auth L],
OA [auth j],
PA [auth j],
UA [auth l]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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IA [auth d],
V [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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EA [auth J],
FA [auth J],
RA [auth j],
SA [auth j]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
AOQ (Subject of Investigation/LOI)
Query on AOQ

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AA [auth J],
NA [auth j]
2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione
C22 H19 Cl O3
KUCQYCKVKVOKAY-CTYIDZIISA-N
AFI (Subject of Investigation/LOI)
Query on AFI

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DA [auth J],
QA [auth j]
2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE
C22 H19 Cl O3
HKIDMHSZRQSXJE-RNMGOYHCSA-N
FES (Subject of Investigation/LOI)
Query on FES

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KA [auth a],
X [auth A]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2025-07-02
    Type: Initial release