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- EMDB-42226: High resolution in-situ structure of typeA supercomplex in respir... -
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Basic information
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Title | High resolution in-situ structure of typeA supercomplex in respiratory chain (I1III2IV1,composite) | |||||||||
![]() | In-situ structure of supercomplex in respiratory chain ( typeA ) | |||||||||
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![]() | in-situ cryo-EM structure / ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex III / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle / respiratory chain complex IV / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zheng W / Zhang K / Zhu J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution in situ structures of mammalian respiratory supercomplexes. Authors: Wan Zheng / Pengxin Chai / Jiapeng Zhu / Kai Zhang / ![]() ![]() Abstract: Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in ...Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: IIIIIV, IIIIIV, IIIIIV and IIIIIV, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 968.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 95.7 KB 95.7 KB | Display Display | ![]() |
Images | ![]() | 81.6 KB | ||
Filedesc metadata | ![]() | 18.9 KB | ||
Others | ![]() ![]() ![]() | 30.7 MB 34.9 MB 30.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ugiMC ![]() 8ud1C ![]() 8ueoC ![]() 8uepC ![]() 8ueqC ![]() 8uerC ![]() 8uesC ![]() 8uetC ![]() 8ueuC ![]() 8uevC ![]() 8uewC ![]() 8uexC ![]() 8ueyC ![]() 8uezC ![]() 8ugdC ![]() 8ugeC ![]() 8ugfC ![]() 8uggC ![]() 8ughC ![]() 8ugjC ![]() 8ugkC ![]() 8uglC ![]() 8ugnC ![]() 8ugpC ![]() 8ugrC 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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Annotation | In-situ structure of supercomplex in respiratory chain ( typeA ) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.417 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: In-situ structure of supercomplex in respiratory chain ( typeA )
File | emd_42226_additional_1.map | ||||||||||||
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Annotation | In-situ structure of supercomplex in respiratory chain ( typeA ) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: In-situ structure of supercomplex in respiratory chain ( typeA )
File | emd_42226_additional_2.map | ||||||||||||
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Annotation | In-situ structure of supercomplex in respiratory chain ( typeA ) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: In-situ structure of supercomplex in respiratory chain ( typeA )
File | emd_42226_additional_3.map | ||||||||||||
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Annotation | In-situ structure of supercomplex in respiratory chain ( typeA ) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : In-situ cryo-EM structure of respiratory supercomplex by directly...
+Supramolecule #1: In-situ cryo-EM structure of respiratory supercomplex by directly...
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #16: NADH:ubiquinone oxidoreductase subunit A9
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #20: NADH:ubiquinone oxidoreductase subunit AB1
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isof...
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #25: NADH:ubiquinone oxidoreductase subunit A13
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 [Sus ...
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #35: NADH:ubiquinone oxidoreductase subunit B2
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #45: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #46: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #47: Cytochrome b
+Macromolecule #48: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #49: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #50: Cytochrome b-c1 complex subunit 7
+Macromolecule #51: Cytochrome b-c1 complex subunit 8
+Macromolecule #52: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #53: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
+Macromolecule #54: Cytochrome b-c1 complex subunit 10
+Macromolecule #55: Cytochrome c oxidase subunit 1
+Macromolecule #56: Cytochrome c oxidase subunit 2
+Macromolecule #57: Cytochrome c oxidase subunit 3
+Macromolecule #58: Cytochrome c oxidase subunit 4
+Macromolecule #59: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #60: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #61: Cytochrome c oxidase subunit 6A2
+Macromolecule #62: Cytochrome c oxidase subunit 6B1
+Macromolecule #63: Cytochrome c oxidase subunit 6C
+Macromolecule #64: Cytochrome c oxidase subunit 7A1, mitochondrial
+Macromolecule #65: Cytochrome c oxidase subunit 7B
+Macromolecule #66: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #67: Cytochrome c oxidase subunit 8
+Macromolecule #68: Cytochrome c oxidase subunit NDUFA4
+Macromolecule #69: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #70: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #71: IRON/SULFUR CLUSTER
+Macromolecule #72: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #73: FLAVIN MONONUCLEOTIDE
+Macromolecule #74: POTASSIUM ION
+Macromolecule #75: CARDIOLIPIN
+Macromolecule #76: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #77: MAGNESIUM ION
+Macromolecule #78: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #79: ZINC ION
+Macromolecule #80: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+Macromolecule #81: N-ACETYLMETHIONINE
+Macromolecule #82: MYRISTIC ACID
+Macromolecule #83: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #84: HEME C
+Macromolecule #85: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #86: HEME-A
+Macromolecule #87: COPPER (II) ION
+Macromolecule #88: SODIUM ION
+Macromolecule #89: DINUCLEAR COPPER ION
+Macromolecule #90: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)MET...
+Macromolecule #91: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)...
+Macromolecule #92: PHOSPHATE ION
+Macromolecule #93: water
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 400000 |