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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4497 | |||||||||
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Title | Ovine respiratory complex I FRC closed class 1 | |||||||||
![]() | Ovine mitochondrial respiratory complex I FRC closed class 1. | |||||||||
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Function / homology | ![]() oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : ...oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / ATP metabolic process / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / circadian rhythm / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / membrane => GO:0016020 / mitochondrial inner membrane / mitochondrial matrix / protein-containing complex binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 480.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 67 KB 67 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 77.3 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Others | ![]() ![]() | 410.4 MB 411.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qc5MC ![]() 4479C ![]() 4480C ![]() 4481C ![]() 4482C ![]() 4493C ![]() 4494C ![]() 4495C ![]() 4496C ![]() 4498C ![]() 4499C ![]() 4500C ![]() 4501C ![]() 4502C ![]() 4505C ![]() 4506C ![]() 4507C ![]() 6q9bC ![]() 6q9dC ![]() 6q9eC ![]() 6qa9C ![]() 6qbxC ![]() 6qc2C ![]() 6qc3C ![]() 6qc4C ![]() 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 complex I FRC closed class 1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 complex I FRC closed class...
File | emd_4497_half_map_1.map | ||||||||||||
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Annotation | Ovine mitochondrial respiratory complex I FRC closed class 1. Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Ovine mitochondrial respiratory complex I FRC closed class...
File | emd_4497_half_map_2.map | ||||||||||||
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Annotation | Ovine mitochondrial respiratory complex I FRC closed class 1. Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Ovine mitochondrial respiratory complex I
+Supramolecule #1: Ovine mitochondrial respiratory complex I
+Macromolecule #1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #2: NDUFV2
+Macromolecule #3: NADH:ubiquinone oxidoreductase core subunit S1
+Macromolecule #4: NDUFS2,NADH:ubiquinone oxidoreductase core subunit S2
+Macromolecule #5: NADH:ubiquinone oxidoreductase core subunit S3
+Macromolecule #6: NADH:ubiquinone oxidoreductase core subunit S7,NDUFS7
+Macromolecule #7: NDUFS8
+Macromolecule #8: NDUFV3
+Macromolecule #9: NDUFS6
+Macromolecule #10: NADH:ubiquinone oxidoreductase subunit S4
+Macromolecule #11: NADH:ubiquinone oxidoreductase subunit A9
+Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #13: NDUFA5
+Macromolecule #14: NADH:ubiquinone oxidoreductase subunit A6
+Macromolecule #15: NDUFA7
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #17: Acyl carrier protein
+Macromolecule #18: NDUFA13
+Macromolecule #19: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #20: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #21: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #22: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #23: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #24: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #25: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #26: NDUFA11
+Macromolecule #27: NADH:ubiquinone oxidoreductase subunit B5
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #29: NDUFB10
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #31: NADH:ubiquinone oxidoreductase subunit S5
+Macromolecule #32: NADH:ubiquinone oxidoreductase subunit A3
+Macromolecule #33: NADH:ubiquinone oxidoreductase subunit B3
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #35: NADH:ubiquinone oxidoreductase subunit B4
+Macromolecule #36: NDUFB6
+Macromolecule #37: NADH:ubiquinone oxidoreductase subunit B7
+Macromolecule #38: NADH:ubiquinone oxidoreductase subunit B9
+Macromolecule #39: NADH:ubiquinone oxidoreductase subunit B2
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #41: NDUFB11
+Macromolecule #42: NDUFC1
+Macromolecule #43: NDUFB1
+Macromolecule #44: NDUFA1
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: FLAVIN MONONUCLEOTIDE
+Macromolecule #47: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #48: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #49: ZINC ION
+Macromolecule #50: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #51: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #52: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
-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 |