[English] 日本語
Yorodumi- PDB-5xtc: Cryo-EM structure of human respiratory complex I transmembrane arm -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xtc | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human respiratory complex I transmembrane arm | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | ELECTRON TRANSPORT / Homo sapiens / Oxidoreductase / Respiratory / Complex | ||||||||||||||||||
Function / homology | Function and homology information protein insertion into mitochondrial inner membrane / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / cellular response to oxygen levels / iron-sulfur cluster assembly complex / response to light intensity / Mitochondrial protein import / mitochondrial large ribosomal subunit binding / gliogenesis ...protein insertion into mitochondrial inner membrane / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / 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 / : / [2Fe-2S] cluster assembly / oxygen sensor activity / cellular response to glucocorticoid stimulus / respiratory chain complex I / iron-sulfur cluster assembly / azurophil granule membrane / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / endopeptidase activator activity / acyl binding / ubiquinone binding / Complex I biogenesis / acyl carrier activity / cellular response to interferon-beta / quinone binding / electron transport coupled proton transport / neurogenesis / Respiratory electron transport / : / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / ionotropic glutamate receptor binding / reactive oxygen species metabolic process / cerebellum development / : / mitochondrial electron transport, NADH to ubiquinone / response to cocaine / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / fatty acid binding / NADH dehydrogenase (ubiquinone) activity / apoptotic signaling pathway / sensory perception of sound / response to nicotine / response to hydrogen peroxide / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / negative regulation of cell growth / fatty acid biosynthetic process / positive regulation of protein catabolic process / NAD binding / 4 iron, 4 sulfur cluster binding / response to ethanol / in utero embryonic development / response to oxidative stress / response to hypoxia / electron transfer activity / mitochondrial inner membrane / nuclear speck / mitochondrial matrix / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / calcium ion binding / Neutrophil degranulation / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / mitochondrion / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytoplasm 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
| ||||||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5xtc.cif.gz | 862.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xtc.ent.gz | 718.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xtc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5xtc_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5xtc_validation.xml.gz | 131.8 KB | Display | |
Data in CIF | 5xtc_validation.cif.gz | 194.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/5xtc ftp://data.pdbj.org/pub/pdb/validation_reports/xt/5xtc | HTTPS FTP |
-Related structure data
Related structure data | 6772MC 6771C 6773C 6774C 6775C 6776C 5xtbC 5xtdC 5xteC 5xthC 5xtiC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 2 types, 2 molecules Qh
#1: Protein/peptide | Mass: 5380.995 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 34-79 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: O75306, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
---|---|
#16: 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 ... , 6 types, 6 molecules SUVWuw
#2: Protein | Mass: 8084.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15239 |
---|---|
#3: Protein | Mass: 9156.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95167 |
#4: Protein | Mass: 14736.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86Y39 |
#5: Protein | Mass: 13589.633 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-144 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J0 |
#27: Protein | Mass: 19853.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51970 |
#29: 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 , 1 types, 1 molecules X
#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 |
---|
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopv
#7: Protein | Mass: 7468.270 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-97 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95178 |
---|---|
#8: Protein | Mass: 9261.605 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-89 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43676 |
#9: Protein | Mass: 16573.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43674 |
#10: Protein | Mass: 15517.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95139 |
#11: Protein | Mass: 18267.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95169 |
#12: Protein | Mass: 20721.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O96000 |
#13: Protein | Mass: 11494.942 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 54-150 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX14 |
#22: Protein | Mass: 6741.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75438 |
#23: Protein | Mass: 15100.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95168 |
#24: Protein | Mass: 21189.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6M9 |
#28: Protein | Mass: 14997.401 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
#14: 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 |
---|---|
#15: 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
#17: 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) |
---|---|
#18: 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) |
#19: 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) |
#20: 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) |
#21: 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) |
#25: 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) |
#26: 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 , 4 types, 19 molecules
#30: Chemical | ChemComp-PLX / ( #31: Chemical | ChemComp-CDL / #32: Chemical | ChemComp-PEE / #33: Chemical | ChemComp-8Q1 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human respiratory complex I transmembrane arm / Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL |
---|---|
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 |
---|---|
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 |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |