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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4496 | |||||||||
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Title | Ovine respiratory supercomplex I+III2 open class 3 | |||||||||
![]() | Ovine mitochondrial respiratory supercomplex I III2 open class 3. | |||||||||
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Function / homology | ![]() mitochondrial respiratory chain complex IV / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone ...mitochondrial respiratory chain complex IV / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / respirasome / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / ATP metabolic process / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / electron transport chain / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / circadian rhythm / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / membrane => GO:0016020 / electron transfer activity / mitochondrial matrix / heme binding / protein-containing complex binding / proteolysis / nucleoplasm / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
![]() | Letts JA / Sazanov LA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk. Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov / ![]() ![]() ![]() Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 480.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 77.9 KB 77.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18 KB | Display | ![]() |
Images | ![]() | 83 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Others | ![]() ![]() | 410.9 MB 410.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 484.4 KB | Display | ![]() |
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Full document | ![]() | 483.5 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qc4MC ![]() 4479C ![]() 4480C ![]() 4481C ![]() 4482C ![]() 4493C ![]() 4494C ![]() 4495C ![]() 4497C ![]() 4498C ![]() 4499C ![]() 4500C ![]() 4501C ![]() 4502C ![]() 4505C ![]() 4506C ![]() 4507C ![]() 6q9bC ![]() 6q9dC ![]() 6q9eC ![]() 6qa9C ![]() 6qbxC ![]() 6qc2C ![]() 6qc3C ![]() 6qc5C ![]() 6qc6C ![]() 6qc7C ![]() 6qc8C ![]() 6qc9C ![]() 6qcaC ![]() 6qcfC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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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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Annotation | Ovine mitochondrial respiratory supercomplex I III2 open class 3. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Ovine mitochondrial respiratory supercomplex I III2 open class...
File | emd_4496_half_map_1.map | ||||||||||||
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Annotation | Ovine mitochondrial respiratory supercomplex I III2 open class 3. Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Ovine mitochondrial respiratory supercomplex I III2 open class...
File | emd_4496_half_map_2.map | ||||||||||||
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Annotation | Ovine mitochondrial respiratory supercomplex I III2 open class 3. Half map 2. | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Ovine mitochondrial respiratory supercomplex I+III2
+Supramolecule #1: Ovine mitochondrial respiratory supercomplex I+III2
+Macromolecule #1: UQCRC1
+Macromolecule #2: Ubiquinol-cytochrome c reductase core protein 2
+Macromolecule #3: Cytochrome b
+Macromolecule #4: Cytochrome c1
+Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #6: UQCRB
+Macromolecule #7: Ubiquinol-cytochrome c reductase complex III subunit VII
+Macromolecule #8: Cytochrome b-c1 complex subunit 6
+Macromolecule #9: UQCRFS1N
+Macromolecule #10: Ubiquinol-cytochrome c reductase, complex III subunit X
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #15: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #16: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #17: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #18: NDUFA11
+Macromolecule #19: NADH:ubiquinone oxidoreductase subunit B5
+Macromolecule #20: Acyl carrier protein
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #22: NDUFB10
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #24: NADH:ubiquinone oxidoreductase subunit S5
+Macromolecule #25: NADH:ubiquinone oxidoreductase subunit A3
+Macromolecule #26: NADH:ubiquinone oxidoreductase subunit B3
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #28: NADH:ubiquinone oxidoreductase subunit B4
+Macromolecule #29: NDUFA13
+Macromolecule #30: NDUFB6
+Macromolecule #31: NADH:ubiquinone oxidoreductase subunit B7
+Macromolecule #32: NADH:ubiquinone oxidoreductase subunit B9
+Macromolecule #33: NADH:ubiquinone oxidoreductase subunit B2
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #35: NDUFB11
+Macromolecule #36: NDUFC1
+Macromolecule #37: NDUFB1
+Macromolecule #38: NDUFA1
+Macromolecule #39: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #40: NDUFV2
+Macromolecule #41: NADH:ubiquinone oxidoreductase core subunit S1
+Macromolecule #42: NDUFS2
+Macromolecule #43: NADH:ubiquinone oxidoreductase core subunit S3
+Macromolecule #44: NDUFS7
+Macromolecule #45: NDUFS8
+Macromolecule #46: NDUFV3
+Macromolecule #47: NDUFS6
+Macromolecule #48: NADH:ubiquinone oxidoreductase subunit S4
+Macromolecule #49: NADH:ubiquinone oxidoreductase subunit A9
+Macromolecule #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #51: NDUFA5
+Macromolecule #52: NADH:ubiquinone oxidoreductase subunit A6
+Macromolecule #53: NDUFA7
+Macromolecule #54: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #55: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #56: HEME C
+Macromolecule #57: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #58: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #59: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #60: IRON/SULFUR CLUSTER
+Macromolecule #61: FLAVIN MONONUCLEOTIDE
+Macromolecule #62: ZINC ION
+Macromolecule #63: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35 | ||||||||||||
Vitrification | Cryogen name: PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 1 / Number real images: 1854 / Average exposure time: 2.0 sec. / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 100000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |