+Open data
-Basic information
Entry | Database: PDB / ID: 5xtd | ||||||||||||||||||
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Title | Cryo-EM structure of human respiratory complex I | ||||||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / Homo sapiens / Oxidoreductase / Respiratory / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||||||||||||||
Function / homology | Function and homology information positive regulation of peptidase activity / protein insertion into mitochondrial inner membrane / response to light intensity / Complex I biogenesis / blastocyst hatching / ubiquinone-6 biosynthetic process / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / cellular response to oxygen levels / Respiratory electron transport ...positive regulation of peptidase activity / protein insertion into mitochondrial inner membrane / response to light intensity / Complex I biogenesis / blastocyst hatching / ubiquinone-6 biosynthetic process / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / cellular response to oxygen levels / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / respiratory gaseous exchange by respiratory system / Mitochondrial protein import / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly / mitochondrial respirasome / cardiac muscle tissue development / NADH dehydrogenase activity / Glyoxylate metabolism and glycine degradation / oxygen sensor activity / cellular respiration / ubiquinone binding / cellular response to glucocorticoid stimulus / acyl binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / mitochondrial ribosome / electron transport coupled proton transport / iron-sulfur cluster assembly / mitochondrial ATP synthesis coupled electron transport / acyl carrier activity / azurophil granule membrane / mitochondrial translation / NADH:ubiquinone reductase (H+-translocating) / sodium ion transport / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / apoptotic mitochondrial changes / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / RHOG GTPase cycle / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / cellular response to interferon-beta / negative regulation of intrinsic apoptotic signaling pathway / respirasome / aerobic respiration / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / response to cAMP / response to organonitrogen compound / ionotropic glutamate receptor binding / substantia nigra development / reactive oxygen species metabolic process / cerebellum development / respiratory electron transport chain / neurogenesis / response to cocaine / regulation of mitochondrial membrane potential / response to nicotine / synaptic membrane / fatty acid binding / apoptotic signaling pathway / mitochondrial membrane / sensory perception of sound / regulation of protein phosphorylation / brain development / response to hydrogen peroxide / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / negative regulation of cell growth / circadian rhythm / positive regulation of protein catabolic process / fatty acid biosynthetic process / NAD binding / positive regulation of fibroblast proliferation / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / response to ethanol / in utero embryonic development / mitochondrial inner membrane / protease binding / electron transfer activity / response to hypoxia / nuclear body / mitochondrial matrix / structural constituent of ribosome / nuclear speck / neuronal cell body / negative regulation of DNA-templated transcription / calcium ion binding / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
Authors | Gu, J. / Wu, M. / Yang, M. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Cell / Year: 2017 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5xtd.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5xtd.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 5xtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/5xtd ftp://data.pdbj.org/pub/pdb/validation_reports/xt/5xtd | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Homo sapiens (human) 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) Homo sapiens (human) / References: UniProt: P56181 |
#14: Protein | Mass: 23430.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) 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) Homo sapiens (human) 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) Homo sapiens (human) 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) Homo sapiens (human) / References: UniProt: O43181 |
#15: Protein | Mass: 24432.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) 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) Homo sapiens (human) 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) Homo sapiens (human) / References: UniProt: O75380 |
#31: Protein | Mass: 12314.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43920 |
-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) Homo sapiens (human) / References: UniProt: P56556 |
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#5: Protein | Mass: 9535.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43678 |
#7: Protein | Mass: 13119.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16718 |
#8: Protein | Mass: 12282.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95182 |
#9: Protein | Mass: 38387.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16795 |
#13: Protein | Mass: 16880.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UI09 |
#17: Protein | Mass: 8084.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15239 |
#19: Protein | Mass: 9156.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95167 |
#20: Protein | Mass: 14736.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86Y39 |
#21: Protein | Mass: 16132.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J0 |
#42: Protein | Mass: 19853.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51970 |
#44: Protein | Mass: 37200.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95299 |
-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) Homo sapiens (human) / References: UniProt: O14561 #12: Protein | | Mass: 75471.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) 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) Homo sapiens (human) / References: UniProt: O95178 |
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#23: Protein | Mass: 9261.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43676 |
#24: Protein | Mass: 16573.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43674 |
#25: Protein | Mass: 15517.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95139 |
#26: Protein | Mass: 18267.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95169 |
#27: Protein | Mass: 20721.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O96000 |
#28: Protein | Mass: 11494.942 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX14 |
#37: Protein | Mass: 6741.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75438 |
#38: Protein | Mass: 15100.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95168 |
#39: Protein | Mass: 21189.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6M9 |
#43: Protein | Mass: 16435.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17568 |
-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) Homo sapiens (human) / References: UniProt: O43677 |
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#30: Protein | Mass: 14209.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95298 |
-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) Homo sapiens (human) 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) Homo sapiens (human) 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) Homo sapiens (human) 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) Homo sapiens (human) 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) Homo sapiens (human) 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) Homo sapiens (human) 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) Homo sapiens (human) References: UniProt: H9PGF0, UniProt: P03886*PLUS, NADH:ubiquinone reductase (H+-translocating) |
-Non-polymers , 8 types, 30 molecules
#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 |
-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: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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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 |