+Open data
-Basic information
Entry | Database: PDB / ID: 5xtb | ||||||||||||||||||
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Title | Cryo-EM structure of human respiratory complex I matrix arm | ||||||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / Respiratory / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||||||||||||||
Function / homology | Function and homology information positive regulation of peptidase activity / protein insertion into mitochondrial inner membrane / 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 ...positive regulation of peptidase activity / protein insertion into mitochondrial inner membrane / 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 / 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 / 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 / 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 / cellular response to interferon-beta / negative regulation of intrinsic apoptotic signaling pathway / aerobic respiration / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / response to cAMP / substantia nigra development / reactive oxygen species metabolic process / respiratory electron transport chain / neurogenesis / regulation of mitochondrial membrane potential / synaptic membrane / fatty acid binding / apoptotic signaling pathway / mitochondrial membrane / regulation of protein phosphorylation / brain development / 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 / mitochondrial inner membrane / protease binding / electron transfer activity / nuclear body / mitochondrial matrix / structural constituent of ribosome / neuronal cell body / negative regulation of DNA-templated transcription / calcium ion binding / ubiquitin protein ligase binding / protein-containing complex binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 | 5xtb.cif.gz | 632.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xtb.ent.gz | 517.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/5xtb ftp://data.pdbj.org/pub/pdb/validation_reports/xt/5xtb | HTTPS FTP |
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-Related structure data
Related structure data | 6771MC 6772C 6773C 6774C 6775C 6776C 5xtcC 5xtdC 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 / Fragment: UNP RESIDUES 27-457 / 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 / Fragment: UNP RESIDUES 74-106 / 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 / Fragment: UNP RESIDUES 36-247 / 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 ... , 6 types, 6 molecules BCLPQT
#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 / Fragment: UNP RESIDUES 58-213 / 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 / Fragment: UNP RESIDUES 58-175 / 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 / Fragment: UNP RESIDUES 43-250 / 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: 43987.625 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 79-463 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: O75306, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#17: Protein | Mass: 10578.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75380 |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 7 types, 7 molecules EFHIJNW
#4: Protein | Mass: 13758.070 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-154 / 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 / Fragment: UNP RESIDUES 14-96 / 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 / Fragment: UNP RESIDUES 4-113 / 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 / Fragment: UNP RESIDUES 40-375 / 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 |
#18: Protein/peptide | Mass: 2560.952 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 7-28 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J0 |
-Protein , 2 types, 2 molecules GM
#6: Protein | Mass: 9845.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561 |
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#12: Protein | Mass: 75471.484 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-716 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P28331, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
-Non-polymers , 5 types, 11 molecules
#19: Chemical | ChemComp-SF4 / #20: Chemical | ChemComp-FMN / | #21: Chemical | ChemComp-8Q1 / | #22: Chemical | ChemComp-NDP / | #23: Chemical | |
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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 matrix arm / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.2 mg/ml / 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167761 / Symmetry type: POINT |