+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 protein insertion into mitochondrial inner membrane / blastocyst hatching / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / respiratory gaseous exchange by respiratory system / cellular response to oxygen levels / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis ...protein insertion into mitochondrial inner membrane / blastocyst hatching / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / respiratory gaseous exchange by respiratory system / cellular response to oxygen levels / iron-sulfur cluster assembly complex / 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 / ubiquinone-6 biosynthetic process / cellular respiration / iron-sulfur cluster assembly / 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 / RHOG GTPase cycle / endopeptidase activator activity / acyl binding / Complex I biogenesis / acyl carrier activity / cellular response to interferon-beta / quinone binding / electron transport coupled proton transport / neurogenesis / Respiratory electron transport / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / response to cAMP / substantia nigra development / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / synaptic membrane / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / fatty acid binding / NADH dehydrogenase (ubiquinone) activity / apoptotic signaling pathway / regulation of protein phosphorylation / circadian rhythm / brain development / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / positive regulation of protein catabolic process / NAD binding / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / protease binding / response to oxidative stress / nuclear body / electron transfer activity / mitochondrial inner membrane / structural constituent of ribosome / mitochondrial matrix / negative regulation of DNA-templated transcription / neuronal cell body / ubiquitin protein ligase binding / calcium ion binding / protein-containing complex binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol 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
Summary document | 5xtb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5xtb_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5xtb_validation.xml.gz | 112.5 KB | Display | |
Data in CIF | 5xtb_validation.cif.gz | 167.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/5xtb ftp://data.pdbj.org/pub/pdb/validation_reports/xt/5xtb | HTTPS FTP |
-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 FIELD |
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 |