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- PDB-7aqq: Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7aqq | ||||||
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Title | Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) | ||||||
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![]() | ELECTRON TRANSPORT / Complex-I | ||||||
Function / homology | ![]() anther dehiscence / vegetative to reproductive phase transition of meristem / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / respiratory chain complex I ...anther dehiscence / vegetative to reproductive phase transition of meristem / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / respiratory chain complex I / regulation of reactive oxygen species metabolic process / plastid / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / : / mitochondrial electron transport, NADH to ubiquinone / : / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / response to salt stress / aerobic respiration / chloroplast / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / mitochondrial inner membrane / copper ion binding / nucleolus / mitochondrion / extracellular region / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å | ||||||
![]() | Klusch, N. / Kuehlbrandt, W. / Yildiz, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I. Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun / ![]() Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 542.7 KB | Display | ![]() |
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PDB format | ![]() | 438.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 101.6 KB | Display | |
Data in CIF | ![]() | 149.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11872MC ![]() 7aqrC ![]() 7aqwC ![]() 7ar7C ![]() 7ar8C ![]() 7ar9C ![]() 7arbC ![]() 7arcC ![]() 7ardC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules AHJLMN
#1: Protein | Mass: 13941.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P92533, NADH:ubiquinone reductase (H+-translocating) |
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#2: Protein | Mass: 36020.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: B5TM92, NADH:ubiquinone reductase (H+-translocating) |
#3: Protein | Mass: 23690.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A2P2CLG1, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 74497.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: B5TM94, NADH:ubiquinone reductase (H+-translocating) |
#6: Protein | Mass: 56055.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: B5TM93, NADH:ubiquinone reductase (H+-translocating) |
#7: Protein | Mass: 55486.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O05000, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase ... , 5 types, 5 molecules KXZae
#4: Protein | Mass: 11165.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#9: Protein | Mass: 11985.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 7349.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 9914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 7 types, 7 molecules Obdfivx
#8: Protein | Mass: 17626.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#12: Protein | Mass: 6810.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 9220.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 11355.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 11808.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 11965.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 27985.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules u
#17: Protein/peptide | Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Gamma carbonic anhydrase ... , 2 types, 2 molecules yz
#20: Protein | Mass: 30102.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9C6B3, Lyases; Carbon-oxygen lyases; Hydro-lyases |
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#21: Protein | Mass: 30010.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9FWR5, Lyases; Carbon-oxygen lyases; Hydro-lyases |
-Non-polymers , 9 types, 10 molecules ![](data/chem/img/UQ9.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/LMN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/PC7.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/PSF.gif)
![](data/chem/img/T7X.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/LMN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/PC7.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/PSF.gif)
![](data/chem/img/T7X.gif)
#22: Chemical | ChemComp-UQ9 / | ||||||||||||||
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#23: Chemical | #24: Chemical | ChemComp-LMN / | #25: Chemical | ChemComp-FE / | #26: Chemical | ChemComp-PC7 / ( | #27: Chemical | ChemComp-ZN / | #28: Chemical | ChemComp-PGT / ( | #29: Chemical | ChemComp-PSF / | #30: Chemical | ChemComp-T7X / | |
-Details
Has ligand of interest | N |
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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: Arabidopsis complex I - membrane core / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.8 |
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: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459177 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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