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Open data
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Basic information
Entry | Database: PDB / ID: 5xtd | ||||||||||||||||||
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Title | Cryo-EM structure of human respiratory complex I | ||||||||||||||||||
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![]() | OXIDOREDUCTASE/ELECTRON TRANSPORT / Homo sapiens / Oxidoreductase / Respiratory / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||||||||||||||
Function / homology | ![]() Complex I biogenesis / protein insertion into mitochondrial inner membrane / blastocyst hatching / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / respiratory gaseous exchange by respiratory system / cellular response to oxygen levels / iron-sulfur cluster assembly complex ...Complex I biogenesis / protein insertion into mitochondrial inner membrane / blastocyst hatching / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / respiratory gaseous exchange by respiratory system / cellular response to oxygen levels / iron-sulfur cluster assembly complex / response to light intensity / Mitochondrial protein import / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / cardiac muscle tissue development / : / [2Fe-2S] cluster assembly / oxygen sensor activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cellular response to glucocorticoid stimulus / ubiquinone-6 biosynthetic process / respiratory chain complex I / cellular respiration / iron-sulfur cluster assembly / azurophil granule membrane / NADH dehydrogenase activity / mitochondrial ribosome / sodium ion transport / mitochondrial translation / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / apoptotic mitochondrial changes / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / RHOG GTPase cycle / endopeptidase activator activity / acyl binding / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / cellular response to interferon-beta / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / response to cAMP / Mitochondrial protein degradation / : / substantia nigra development / ionotropic glutamate receptor binding / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / neurogenesis / cerebellum development / regulation of mitochondrial membrane potential / response to cocaine / synaptic membrane / fatty acid binding / mitochondrial membrane / apoptotic signaling pathway / sensory perception of sound / regulation of protein phosphorylation / response to nicotine / brain development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / circadian rhythm / positive regulation of protein catabolic process / NAD binding / positive regulation of fibroblast proliferation / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / protease binding / response to ethanol / in utero embryonic development / response to oxidative stress / mitochondrial inner membrane / electron transfer activity / response to hypoxia / nuclear body / nuclear speck / structural constituent of ribosome / mitochondrial matrix / negative regulation of DNA-templated transcription / neuronal cell body / ubiquitin protein ligase binding / calcium ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
![]() | Gu, J. / Wu, M. / Yang, M. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Architecture of Human Mitochondrial Respiratory Megacomplex IIIIIV. Authors: Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang / ![]() Abstract: The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, ...The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-IIIIIV (MCIIIIIV) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCIIIIIV forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6773MC ![]() 6771C ![]() 6772C ![]() 6774C ![]() 6775C ![]() 6776C ![]() 5xtbC ![]() 5xtcC ![]() 5xteC ![]() 5xthC ![]() 5xtiC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules AKO
#1: Protein | Mass: 47323.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P49821, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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#10: Protein/peptide | Mass: 3900.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 23430.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P19404, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules BCLPQTh
#2: Protein | Mass: 20314.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: O00217, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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#3: Protein | Mass: 17887.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: O75251, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#11: Protein | Mass: 13721.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 24432.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: O75489, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#16: Protein | Mass: 49236.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: O75306, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#18: Protein | Mass: 10578.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#31: Protein | Mass: 12314.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 12 molecules EFHIJNSUVWuw
#4: Protein | Mass: 13758.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#5: Protein | Mass: 9535.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 13119.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 12282.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 38387.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 16880.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein | Mass: 8084.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#19: Protein | Mass: 9156.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#20: Protein | Mass: 14736.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: Protein | Mass: 16132.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 19853.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#44: Protein | Mass: 37200.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 2 types, 3 molecules GXM
#6: Protein | Mass: 9845.247 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | | Mass: 75471.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P28331, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopv
#22: Protein | Mass: 7468.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#23: Protein | Mass: 9261.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#24: Protein | Mass: 16573.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 15517.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 18267.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#27: Protein | Mass: 20721.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 11494.942 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 6741.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#38: Protein | Mass: 15100.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#39: Protein | Mass: 21189.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 16435.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules fg
#29: Protein/peptide | Mass: 5704.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#30: Protein | Mass: 14209.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijklmrs
#32: Protein | Mass: 39007.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q4GRX1, UniProt: P03891*PLUS, NADH:ubiquinone reductase (H+-translocating) |
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#33: Protein | Mass: 13147.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: B9EE38, UniProt: P03897*PLUS, NADH:ubiquinone reductase (H+-translocating) |
#34: Protein | Mass: 10702.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: V9JN72, UniProt: P03901*PLUS, NADH:ubiquinone reductase (H+-translocating) |
#35: Protein | Mass: 67096.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: X5BVZ3, UniProt: P03915*PLUS, NADH:ubiquinone reductase (H+-translocating) |
#36: Protein | Mass: 18660.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q8HAX7, UniProt: P03923*PLUS, NADH:ubiquinone reductase (H+-translocating) |
#40: Protein | Mass: 51689.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: B2XJG5, UniProt: P03905*PLUS, NADH:ubiquinone reductase (H+-translocating) |
#41: Protein | Mass: 35621.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: H9PGF0, UniProt: P03886*PLUS, NADH:ubiquinone reductase (H+-translocating) |
-Non-polymers , 8 types, 30 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/PEE.gif)
#45: Chemical | ChemComp-SF4 / #46: Chemical | ChemComp-FMN / | #47: Chemical | ChemComp-PLX / ( #48: Chemical | #49: Chemical | ChemComp-NDP / | #50: Chemical | #51: Chemical | ChemComp-CDL / #52: Chemical | ChemComp-PEE / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human respiratory complex I / Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167761 / Symmetry type: POINT |