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- EMDB-15315: Complex III2 from Yarrowia lipolytica, ascorbate-reduced, b-position -
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Open data
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Basic information
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Title | Complex III2 from Yarrowia lipolytica, ascorbate-reduced, b-position | |||||||||
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Function / homology | ![]() mitochondrial processing peptidase complex / mitochondrial processing peptidase / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista ...mitochondrial processing peptidase complex / mitochondrial processing peptidase / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / nuclear periphery / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Wieferig JP / Kuhlbrandt W | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III by cryo-EM. Authors: Jan Philip Wieferig / Werner Kühlbrandt / ![]() Abstract: 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 ...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. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 164 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.2 KB 26.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 62.1 KB | ||
Others | ![]() ![]() | 141 MB 141 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ab9MC ![]() 8ab6C ![]() 8ab7C ![]() 8ab8C ![]() 8abaC ![]() 8abbC ![]() 8abeC ![]() 8abfC ![]() 8abgC ![]() 8abhC ![]() 8abiC ![]() 8abjC ![]() 8abkC ![]() 8ablC ![]() 8abmC ![]() 8ac3C ![]() 8ac4C ![]() 8ac5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.831 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_15315_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15315_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Complex III2, ascorbate-reduced, b-position
+Supramolecule #1: Complex III2, ascorbate-reduced, b-position
+Macromolecule #1: Cytochrome b
+Macromolecule #2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #3: Cytochrome b-c1 complex subunit 7
+Macromolecule #4: YALI0F24673p
+Macromolecule #5: YALI0A14806p
+Macromolecule #6: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #7: YALI0A17468p
+Macromolecule #8: Cytochrome b-c1 complex subunit 8
+Macromolecule #9: Complex III subunit 9
+Macromolecule #10: YALI0C12210p
+Macromolecule #11: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #12: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #13: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #14: CARDIOLIPIN
+Macromolecule #15: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #17: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE
+Macromolecule #18: HEME C
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |