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- PDB-5xti: Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2 -
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Basic information
Entry | Database: PDB / ID: 5xti | ||||||||||||||||||
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Title | Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2 | ||||||||||||||||||
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![]() | OXIDOREDUCTASE/ELECTRON TRANSPORT / Homo sapiens / Oxidoreductase / Respiratory / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||||||||||||||
Function / homology | ![]() subthalamus development / pons development / cerebellar Purkinje cell layer development / Complex I biogenesis / blastocyst hatching / pyramidal neuron development / TP53 Regulates Metabolic Genes / protein lipoylation / response to mercury ion / Mitochondrial Fatty Acid Beta-Oxidation ...subthalamus development / pons development / cerebellar Purkinje cell layer development / Complex I biogenesis / blastocyst hatching / pyramidal neuron development / TP53 Regulates Metabolic Genes / protein lipoylation / response to mercury ion / Mitochondrial Fatty Acid Beta-Oxidation / mitochondrial respiratory chain complex III assembly / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / thalamus development / protein insertion into mitochondrial inner membrane / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory gaseous exchange by respiratory system / cellular response to oxygen levels / iron-sulfur cluster assembly complex / Mitochondrial protein import / : / mitochondrial large ribosomal subunit binding / regulation of oxidative phosphorylation / Respiratory electron transport / gliogenesis / Glyoxylate metabolism and glycine degradation / : / response to alkaloid / neural precursor cell proliferation / cardiac muscle tissue development / cytochrome-c oxidase / : / [2Fe-2S] cluster assembly / oxidative phosphorylation / oxygen sensor activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / quinol-cytochrome-c reductase / respiratory chain complex I / response to copper ion / deoxynucleoside kinase activity / response to glucagon / cellular respiration / ubiquinone-6 biosynthetic process / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / azurophil granule membrane / iron-sulfur cluster assembly / midbrain development / mitochondrial ribosome / sodium ion transport / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial translation / response to cobalamin / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / apoptotic mitochondrial changes / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / : / proton motive force-driven mitochondrial ATP synthesis / endopeptidase activator activity / RHOG GTPase cycle / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / response to hyperoxia / cellular response to interferon-beta / acyl carrier activity / quinone binding / animal organ regeneration / electron transport coupled proton transport / response to cadmium ion / ATP synthesis coupled electron transport / enzyme regulator activity / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / response to cAMP / : / Mitochondrial protein degradation / substantia nigra development / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / cerebellum development / neurogenesis / regulation of mitochondrial membrane potential / synaptic membrane / response to activity / generation of precursor metabolites and energy / central nervous system development Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17.4 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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PDBx/mmCIF format | ![]() | 4.4 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 3.9 MB | Display | ![]() |
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Full document | ![]() | 4.2 MB | Display | |
Data in XML | ![]() | 484.6 KB | Display | |
Data in CIF | ![]() | 830.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6776MC ![]() 6771C ![]() 6772C ![]() 6773C ![]() 6774C ![]() 6775C ![]() 5xtbC ![]() 5xtcC ![]() 5xtdC ![]() 5xteC ![]() 5xthC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
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Components
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 6 molecules ABAKBKOBO
#1: Protein | Mass: 47323.938 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-457 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P49821, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase #10: Protein/peptide | Mass: 3900.312 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 74-106 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 23430.881 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 36-247 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P19404, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 14 molecules BBBCBCLBLPBPQBQTBThBh
#2: Protein | Mass: 20314.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: O00217, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase #3: Protein | Mass: 17887.928 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 58-213 / 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.: 2 / Fragment: UNP RESIDUES 58-175 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | Mass: 24432.656 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 43-250 / 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.: 2 / 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.: 2 / Fragment: UNP RESIDUES 29-123 / Source method: isolated from a natural source / Source: (natural) ![]() #31: Protein | Mass: 12314.254 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-105 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 24 molecules EBEFBFHBHIBIJBJNBNSBSUBUVBVWBWuBuwBw
#4: Protein | Mass: 13758.070 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 42-154 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 9535.905 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 14-96 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 13119.208 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 5-116 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 12282.051 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 4-113 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 38387.594 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 40-376 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | Mass: 16880.068 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-144 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | Mass: 8084.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | Mass: 9156.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #20: Protein | Mass: 14736.853 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #21: Protein | Mass: 16132.570 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 7-144 / Source method: isolated from a natural source / Source: (natural) ![]() #42: Protein | Mass: 19853.736 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 4-172 / Source method: isolated from a natural source / Source: (natural) ![]() #44: Protein | Mass: 37200.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein , 4 types, 10 molecules GXBGBXMBMAHAUAJAV
#6: Protein | Mass: 9845.247 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 72-196 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 75471.484 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-716 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P28331, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase #65: Protein | Mass: 27388.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #66: Protein | Mass: 42543.016 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-479 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 22 molecules YBYZBZaBabBbcBcdBdeBenBnoBopBpvBv
#22: Protein | Mass: 7468.270 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 39-97 / Source method: isolated from a natural source / Source: (natural) ![]() #23: Protein | Mass: 9261.605 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 10-89 / Source method: isolated from a natural source / Source: (natural) ![]() #24: Protein | Mass: 16573.160 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 52-189 / Source method: isolated from a natural source / Source: (natural) ![]() #25: Protein | Mass: 15008.635 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 3-126 / Source method: isolated from a natural source / Source: (natural) ![]() #26: Protein | Mass: 18267.562 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 34-186 / Source method: isolated from a natural source / Source: (natural) ![]() #27: Protein | Mass: 20721.650 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-171 / Source method: isolated from a natural source / Source: (natural) ![]() #28: Protein | Mass: 11494.942 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 54-150 / Source method: isolated from a natural source / Source: (natural) ![]() #37: Protein | Mass: 6741.883 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 3-58 / Source method: isolated from a natural source / Source: (natural) ![]() #38: Protein | Mass: 15100.399 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #39: Protein | Mass: 21189.141 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 8-179 / Source method: isolated from a natural source / Source: (natural) ![]() #43: Protein | Mass: 14997.401 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 3-124 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 4 molecules fBfgBg
#29: Protein/peptide | Mass: 5704.602 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 28-74 / Source method: isolated from a natural source / Source: (natural) ![]() #30: Protein | Mass: 14209.521 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-NADH-ubiquinone oxidoreductase chain ... , 7 types, 14 molecules iBijBjkBklBlmBmrBrsBs
#32: Protein | Mass: 39007.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q4GRX1, UniProt: P03891*PLUS, NADH:ubiquinone reductase (H+-translocating) #33: Protein | Mass: 13147.871 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-115 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: B9EE38, NADH:ubiquinone reductase (H+-translocating) #34: Protein | Mass: 10702.086 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-97 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: V9JN72, NADH:ubiquinone reductase (H+-translocating) #35: Protein | Mass: 67096.023 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q8HAX7, NADH:ubiquinone reductase (H+-translocating) #40: Protein | Mass: 51689.688 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: H9PGF0, NADH:ubiquinone reductase (H+-translocating) |
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-Cytochrome c oxidase subunit ... , 13 types, 26 molecules xBxyByzBz0B01B12B23B34B45B56B67B78B89B9
#45: Protein | Mass: 57065.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #46: Protein | Mass: 26040.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #47: Protein | Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #48: Protein | Mass: 16913.367 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-169 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #49: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #50: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #51: Protein | Mass: 9452.687 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 13-96 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #52: Protein | Mass: 8925.979 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 12-86 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #53: Protein | Mass: 8494.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #54: Protein | Mass: 6286.220 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 22-77 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #55: Protein/peptide | Mass: 5442.168 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-78 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #56: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #57: Protein/peptide | Mass: 4738.523 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-67 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules AAANABAOACAPADAQAEARAFASAGATAKAWALAY
#58: Protein | Mass: 9791.181 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #59: Protein | Mass: 5893.814 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-57 / Source method: isolated from a natural source / Source: (natural) ![]() #60: Protein | Mass: 21645.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #61: Protein | Mass: 7189.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #62: Protein | Mass: 8861.742 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 18-91 / Source method: isolated from a natural source / Source: (natural) ![]() #63: Protein | Mass: 13037.842 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-111 / Source method: isolated from a natural source / Source: (natural) ![]() #64: Protein | Mass: 5958.912 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-52 / Source method: isolated from a natural source / Source: (natural) ![]() #67: Protein | Mass: 44946.582 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-453 / Source method: isolated from a natural source / Source: (natural) ![]() #68: Protein | Mass: 49181.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 14 types, 100 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/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HEM.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/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HEM.gif)
#69: Chemical | ChemComp-SF4 / #70: Chemical | #71: Chemical | ChemComp-PLX / ( #72: Chemical | ChemComp-8Q1 / #73: Chemical | #74: Chemical | ChemComp-FES / #75: Chemical | ChemComp-CDL / #76: Chemical | ChemComp-PEE / #77: Chemical | ChemComp-CU / #78: Chemical | #79: Chemical | ChemComp-HEA / #80: Chemical | #81: Chemical | #82: Chemical | ChemComp-HEM / |
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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 chain megacomplex-I2III2IV2 / Type: COMPLEX / Entity ID: #1-#68 / Source: NATURAL |
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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
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 17.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8600 / Symmetry type: POINT |