+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4493 | |||||||||
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Title | Ovine respiratory supercomplex I+III2 closed class. | |||||||||
Map data | Ovine mitochondrial respiratory supercomplex I III2 closed class. | |||||||||
Sample |
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Keywords | supercomplex / cellular respiration / mitochondria / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information : / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / NADH dehydrogenase activity / : / mitochondrial respiratory chain complex I assembly ...: / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / NADH dehydrogenase activity / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / membrane => GO:0016020 / : / ATP metabolic process / respiratory electron transport chain / reactive oxygen species metabolic process / FAD binding / regulation of mitochondrial membrane potential / electron transport chain / metalloendopeptidase activity / mitochondrial intermembrane space / 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 / electron transfer activity / oxidoreductase activity / mitochondrial matrix / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / proteolysis / nucleoplasm / metal ion binding Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Letts JA / Sazanov LA | |||||||||
Funding support | Austria, 1 items
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Citation | Journal: Mol Cell / Year: 2019 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4493.map.gz | 480.7 MB | EMDB map data format | |
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Header (meta data) | emd-4493-v30.xml emd-4493.xml | 81.4 KB 81.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4493_fsc.xml | 17.9 KB | Display | FSC data file |
Images | emd_4493.png | 101.2 KB | ||
Masks | emd_4493_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-4493.cif.gz | 16.2 KB | ||
Others | emd_4493_half_map_1.map.gz emd_4493_half_map_2.map.gz | 410.8 MB 410.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4493 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4493 | HTTPS FTP |
-Validation report
Summary document | emd_4493_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_4493_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_4493_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | emd_4493_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4493 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4493 | HTTPS FTP |
-Related structure data
Related structure data | 6qbxMC 4479C 4480C 4481C 4482C 4494C 4495C 4496C 4497C 4498C 4499C 4500C 4501C 4502C 4505C 4506C 4507C 6q9bC 6q9dC 6q9eC 6qa9C 6qc2C 6qc3C 6qc4C 6qc5C 6qc6C 6qc7C 6qc8C 6qc9C 6qcaC 6qcfC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4493.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ovine mitochondrial respiratory supercomplex I III2 closed class. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
File | emd_4493_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Ovine mitochondrial respiratory supercomplex I III2 closed class....
File | emd_4493_half_map_1.map | ||||||||||||
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Annotation | Ovine mitochondrial respiratory supercomplex I III2 closed class. Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Ovine mitochondrial respiratory supercomplex I III2 closed class....
File | emd_4493_half_map_2.map | ||||||||||||
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Annotation | Ovine mitochondrial respiratory supercomplex I III2 closed class. Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ovine mitochondrial supercomplex I+III2
+Supramolecule #1: Ovine mitochondrial supercomplex I+III2
+Macromolecule #1: Ubiquinol-cytochrome c reductase core protein 1
+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: Cytochrome b-c1 complex subunit 7
+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 dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #12: NDUFV2
+Macromolecule #13: NADH:ubiquinone oxidoreductase core subunit S1
+Macromolecule #14: NDUFS2
+Macromolecule #15: NADH:ubiquinone oxidoreductase core subunit S3
+Macromolecule #16: NDUFS7
+Macromolecule #17: NDUFS8
+Macromolecule #18: NDUFV3
+Macromolecule #19: NDUFS6
+Macromolecule #20: NADH:ubiquinone oxidoreductase subunit S4
+Macromolecule #21: NADH:ubiquinone oxidoreductase subunit A9
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #23: NDUFA5
+Macromolecule #24: NADH:ubiquinone oxidoreductase subunit A6
+Macromolecule #25: NDUFA7
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #27: Acyl carrier protein
+Macromolecule #28: NDUFA13
+Macromolecule #29: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #30: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #31: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #32: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #33: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #34: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #35: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #36: NDUFA11
+Macromolecule #37: NADH:ubiquinone oxidoreductase subunit B5
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #39: NDUFB10
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #41: NADH:ubiquinone oxidoreductase subunit S5
+Macromolecule #42: NADH:ubiquinone oxidoreductase subunit A3
+Macromolecule #43: NADH:ubiquinone oxidoreductase subunit B3
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #45: NADH:ubiquinone oxidoreductase subunit B4
+Macromolecule #46: NDUFB6
+Macromolecule #47: NADH:ubiquinone oxidoreductase subunit B7
+Macromolecule #48: NADH:ubiquinone oxidoreductase subunit B9
+Macromolecule #49: NADH:ubiquinone oxidoreductase subunit B2
+Macromolecule #50: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #51: NDUFB11
+Macromolecule #52: NDUFC1
+Macromolecule #53: NDUFB1
+Macromolecule #54: NDUFA1
+Macromolecule #55: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #56: HEME C
+Macromolecule #57: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #58: IRON/SULFUR CLUSTER
+Macromolecule #59: FLAVIN MONONUCLEOTIDE
+Macromolecule #60: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #61: ZINC ION
+Macromolecule #62: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #63: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #64: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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. |
-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: FIELD EMISSION GUN |
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 |