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- PDB-7arb: Cryo-EM structure of Arabidopsis thaliana Complex-I (complete com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7arb | ||||||
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Title | Cryo-EM structure of Arabidopsis thaliana Complex-I (complete composition) | ||||||
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![]() | ELECTRON TRANSPORT / Complex-I | ||||||
Function / homology | ![]() anther dehiscence / vegetative to reproductive phase transition of meristem / cold acclimation / 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 ...anther dehiscence / vegetative to reproductive phase transition of meristem / cold acclimation / 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 / ubiquinone-6 biosynthetic process / regulation of reactive oxygen species metabolic process / response to osmotic stress / plastid / cobalt ion binding / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / : / mitochondrial electron transport, NADH to ubiquinone / : / chloroplast thylakoid membrane / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / acyl binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / response to salt stress / aerobic respiration / respiratory electron transport chain / chloroplast / mitochondrial membrane / electron transport chain / carbonate dehydratase activity / mitochondrial intermembrane space / transmembrane transport / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / peroxisome / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / carbohydrate metabolic process / mitochondrial matrix / copper ion binding / protein-containing complex binding / nucleolus / mitochondrion / zinc ion binding / 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: 3.41 Å | ||||||
![]() | Klusch, N. / Kuelbrandt, 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 | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 192.4 KB | Display | |
Data in CIF | ![]() | 295.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11878MC ![]() 7aqqC ![]() 7aqrC ![]() 7aqwC ![]() 7ar7C ![]() 7ar8C ![]() 7ar9C ![]() 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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Components
+NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules AHJLMN
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules BCGIQRe
+NADH dehydrogenase subunit ... , 2 types, 2 molecules DK
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules EF
+Protein , 11 types, 11 molecules Obcdfgimrvx
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 6 types, 6 molecules PSWXZa
+Acyl carrier protein ... , 2 types, 2 molecules TU
+Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 2 types, 2 molecules Vq
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 6 types, 6 molecules jklnop
+Protein/peptide , 1 types, 1 molecules u
+Gamma carbonic anhydrase ... , 2 types, 2 molecules yz
+Non-polymers , 14 types, 25 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/UQ9.gif)
![](data/chem/img/LMN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/PC7.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/T7X.gif)
![](data/chem/img/PSF.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/UQ9.gif)
![](data/chem/img/LMN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/PC7.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/T7X.gif)
![](data/chem/img/PSF.gif)
+Details
-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: Cryo-EM structure of Arabidopsis thaliana Complex-I (complete composition) Type: COMPLEX / Entity ID: #1-#47 / 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: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459177 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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