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Yorodumi- PDB-7arb: Cryo-EM structure of Arabidopsis thaliana Complex-I (complete com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7arb | ||||||
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Title | Cryo-EM structure of Arabidopsis thaliana Complex-I (complete composition) | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Complex-I | ||||||
Function / homology | Function and homology information anther dehiscence / vegetative to reproductive phase transition of meristem / cold acclimation / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / 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 / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / 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 / cobalt ion binding / response to osmotic stress / acyl carrier activity / plastid / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / protein homotrimerization / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / response to salt stress / respiratory electron transport chain / chloroplast / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / carbohydrate metabolic process / mitochondrial matrix / copper ion binding / nucleolus / mitochondrion / zinc ion binding / extracellular region / membrane / metal ion binding / nucleus / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å | ||||||
Authors | Klusch, N. / Kuelbrandt, W. / Yildiz, O. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Plant Cell / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7arb.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7arb.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7arb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/7arb ftp://data.pdbj.org/pub/pdb/validation_reports/ar/7arb | HTTPS FTP |
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-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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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
+Details
-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: 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: Arabidopsis thaliana (thale cress) |
Buffer solution | pH: 7.8 |
Specimen | 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-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 | ||||||||||||||||||||||||
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