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Structure paper

TitleAnalysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III by cryo-EM.
Journal, issue, pagesIUCrJ, Vol. 10, Issue Pt 1, Page 27-37, Year 2023
Publish dateJan 1, 2023
AuthorsJan Philip Wieferig / Werner Kühlbrandt /
PubMed AbstractMovement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III (CIII) of the respiratory chain as it bridges a gap in the cofactor chain ...Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III (CIII) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII with a reduced high-potential chain increased the occupancy of the Q site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
External linksIUCrJ / PubMed:36598500 / PubMed Central
MethodsEM (single particle)
Resolution2.0 - 3.7 Å
Structure data

EMDB-15312, PDB-8ab6:
Complex III2 from Yarrowia lipolytica, combined datasets, consensus refinement
Method: EM (single particle) / Resolution: 2.0 Å

EMDB-15313, PDB-8ab7:
Complex III2 from Yarrowia lipolytica, atovaquone and antimycin A bound
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-15314, PDB-8ab8:
Complex III2, b-position, with decylubiquinone and ascorbate-reduced
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-15315, PDB-8ab9:
Complex III2 from Yarrowia lipolytica, ascorbate-reduced, b-position
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-15316, PDB-8aba:
Complex III2 from Yarrowia lipolytica, ascorbate-reduced, int-position
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-15317, PDB-8abb:
Complex III2 from Yarrowia lipolytica, ascorbate-reduced, c-position
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-15318, PDB-8abe:
Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, b-position
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-15319, PDB-8abf:
Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, int-position
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-15320, PDB-8abg:
Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, c-position
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-15321, PDB-8abh:
Complex III2 from Yarrowia lipolytica, antimycin A bound, b-position
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-15322, PDB-8abi:
Complex III2 from Yarrowia lipolytica,antimycin A bound, int-position
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-15323, PDB-8abj:
Complex III2 from Yarrowia lipolytica, antimycin A bound, c-position
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-15324, PDB-8abk:
Complex III2 from Yarrowia lipolytica, decylubiquinol bound, b-position
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-15325, PDB-8abl:
Complex III2 from Yarrowia lipolytica, with decylubiquinol and antimycin A, consensus refinement
Method: EM (single particle) / Resolution: 2.1 Å

EMDB-15326, PDB-8abm:
Complex III2 from Yarrowia lipolytica, apo, b-position
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-15332, PDB-8ac3:
Complex III2 from Yarrowia lipolytica, apo, int-position
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-15333, PDB-8ac4:
Complex III2 from Yarrowia lipolytica, apo, c-position
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-15334, PDB-8ac5:
Complex III2 from Yarrowia lipolytica, with decylubiquinol, oxidised, b-position
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

ChemComp-XP4:
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / DMPA, phospholipid*YM

ChemComp-HEC:
HEME C

ChemComp-HOH:
WATER

ChemComp-AWB:
[(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate

ChemComp-AOQ:
2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione / medication, Antimicrobial*YM

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-DCQ:
2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione

Source
  • yarrowia lipolytica (yeast)
KeywordsMEMBRANE PROTEIN / oxidoreductase / electron transport chain / inhibitor

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