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- EMDB-50210: Subtomogram average of the Chlamydomonas reinhardtii mitochondria... -
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Basic information
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Title | Subtomogram average of the Chlamydomonas reinhardtii mitochondrial respirasome - C2 symmetry | |||||||||
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![]() | respirasome / alga / respiration / mitochondria / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() NADH:ubiquinone reductase (H+-translocating) / TIM22 mitochondrial import inner membrane insertion complex / quinol-cytochrome-c reductase / NADH dehydrogenase / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / NADH dehydrogenase complex / ubiquinone biosynthetic process / respiratory chain complex IV / mitochondrial envelope ...NADH:ubiquinone reductase (H+-translocating) / TIM22 mitochondrial import inner membrane insertion complex / quinol-cytochrome-c reductase / NADH dehydrogenase / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / NADH dehydrogenase complex / ubiquinone biosynthetic process / respiratory chain complex IV / mitochondrial envelope / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / oxidoreductase activity, acting on NAD(P)H / mitochondrial electron transport, cytochrome c to oxygen / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / acyl binding / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / phosphopantetheine binding / protein transmembrane transporter activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / copper ion binding / heme binding / protein-containing complex binding / mitochondrion / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 5.44 Å | |||||||||
![]() | Waltz F / Righetto R / Kotecha A / Engel BD | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: In-cell architecture of the mitochondrial respiratory chain. Authors: Florent Waltz / Ricardo D Righetto / Lorenz Lamm / Thalia Salinas-Giegé / Ron Kelley / Xianjun Zhang / Martin Obr / Sagar Khavnekar / Abhay Kotecha / Benjamin D Engel / ![]() ![]() ![]() ![]() ![]() Abstract: Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, ...Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (Å) resolution structure showing binding of electron carrier cytochrome . Combined with single-particle cryo-electron microscopy at 2.4-Å resolution, we model how the respiratory complexes organize inside native mitochondria. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 94.5 KB 94.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.2 KB | Display | ![]() |
Images | ![]() | 93.8 KB | ||
Masks | ![]() | 91.1 MB | ![]() | |
Filedesc metadata | ![]() | 19.9 KB | ||
Others | ![]() ![]() ![]() | 49.6 MB 70 MB 70.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 988.8 KB | Display | ![]() |
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Full document | ![]() | 988.4 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9f62MC ![]() 9f5xC ![]() 9f5yC ![]() 9f5zC ![]() 9f60C ![]() 9f61C C: citing same article ( M: atomic model generated by this map |
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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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.91 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Output of RELION LocRes
File | emd_50210_additional_1.map | ||||||||||||
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Annotation | Output of RELION LocRes | ||||||||||||
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-Half map: #2
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Density Histograms |
-Half map: #1
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Sample components
+Entire : Chlamydomonas reinhardtii
+Supramolecule #1: Chlamydomonas reinhardtii
+Macromolecule #1: Cytochrome b
+Macromolecule #2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #3: Cytochrome c1
+Macromolecule #4: Complex III subunit 9
+Macromolecule #5: Cytochrome b-c1 complex subunit 6
+Macromolecule #6: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8
+Macromolecule #7: MPP-Beta
+Macromolecule #8: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10
+Macromolecule #9: Alpha-MPP
+Macromolecule #10: Cytochrome b-c1 complex subunit 7
+Macromolecule #11: Cytochrome c oxidase subunit 1
+Macromolecule #12: Cytochrome c oxidase polypeptide II
+Macromolecule #13: cytochrome-c oxidase
+Macromolecule #14: Cytochrome c oxidase subunit 3
+Macromolecule #15: Cox5b
+Macromolecule #16: Cox5c
+Macromolecule #17: Cox6a
+Macromolecule #18: Cox6b
+Macromolecule #19: Cox7c
+Macromolecule #20: Cytochrome c oxidase subunit
+Macromolecule #21: Cox7a
+Macromolecule #22: CoxIn
+Macromolecule #23: NADH:ubiquinone oxidoreductase 24 kD subunit
+Macromolecule #24: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #25: NADH:ubiquinone oxidoreductase 78 kDa subunit
+Macromolecule #26: NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein
+Macromolecule #27: NADH:ubiquinone oxidoreductase 49 kD subunit
+Macromolecule #28: NADH:ubiquinone oxidoreductase subunit 10
+Macromolecule #29: NADH:ubiquinone oxidoreductase subunit 8
+Macromolecule #30: B14.5a
+Macromolecule #31: Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit
+Macromolecule #32: Acyl carrier protein
+Macromolecule #33: NADH:ubiquinone oxidoreductase B14 subunit
+Macromolecule #34: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #35: NADH:ubiquinone oxidoreductase 13 kD-like subunit
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #37: NADH:ubiquinone oxidoreductase B8 subunit
+Macromolecule #38: Putative NADH:ubiquinone oxidoreductase 39 kDa subunit
+Macromolecule #39: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #40: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #41: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #42: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #43: NADH dehydrogenase subunit 4L
+Macromolecule #44: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #45: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #46: ASHI
+Macromolecule #47: P9
+Macromolecule #48: KFYI
+Macromolecule #49: AGGG
+Macromolecule #50: ESSS
+Macromolecule #51: B9
+Macromolecule #52: Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunit
+Macromolecule #53: Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunit
+Macromolecule #54: Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunit
+Macromolecule #55: Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit
+Macromolecule #56: Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunit
+Macromolecule #57: NADH:ubiquinone oxidoreductase 15 kDa subunit-like
+Macromolecule #58: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #59: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #60: NADH:ubiquinone oxidoreductase 20,9 kD-like subunit
+Macromolecule #61: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #62: Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunit
+Macromolecule #63: Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunit
+Macromolecule #64: Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunit
+Macromolecule #65: Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunit
+Macromolecule #66: Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunit
+Macromolecule #67: CAG2 - CA-like
+Macromolecule #68: CAG1
+Macromolecule #69: P10
+Macromolecule #70: Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunit
+Macromolecule #71: NUOP8
+Macromolecule #72: NUOP7
+Macromolecule #73: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #74: HEME C
+Macromolecule #75: ZINC ION
+Macromolecule #76: HEME-A
+Macromolecule #77: COPPER (II) ION
+Macromolecule #78: MAGNESIUM ION
+Macromolecule #79: DINUCLEAR COPPER ION
+Macromolecule #80: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #81: FLAVIN MONONUCLEOTIDE
+Macromolecule #82: IRON/SULFUR CLUSTER
+Macromolecule #83: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #84: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #85: CROTONYL COENZYME A
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X |
Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |