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Yorodumi- PDB-7ar7: Cryo-EM structure of Arabidopsis thaliana complex-I (open conform... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ar7 | ||||||
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Title | Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation) | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Complex-I Arabidopsis | ||||||
Function / homology | Function and homology information anther dehiscence / vegetative to reproductive phase transition of meristem / cold acclimation / 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 / cold acclimation / 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 / response to osmotic stress / NADH dehydrogenase activity / plastid / cobalt ion binding / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / response to salt stress / respiratory electron transport chain / chloroplast / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / carbonate dehydratase activity / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / transmembrane transport / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / peroxisome / 4 iron, 4 sulfur cluster binding / carbohydrate metabolic process / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / nucleolus / mitochondrion / zinc ion binding / extracellular region / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å | ||||||
Authors | Klusch, N. / Kuelbrandt, W. | ||||||
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 | 7ar7.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ar7.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7ar7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ar7_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7ar7_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7ar7_validation.xml.gz | 200.8 KB | Display | |
Data in CIF | 7ar7_validation.cif.gz | 304.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/7ar7 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/7ar7 | HTTPS FTP |
-Related structure data
Related structure data | 11875MC 7aqqC 7aqrC 7aqwC 7ar8C 7ar9C 7arbC 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 ... , 7 types, 7 molecules AHJKLMN
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 8 types, 8 molecules BCDGIQRe
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules EF
+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
+Protein/peptide , 4 types, 4 molecules bruv
+Protein , 7 types, 7 molecules cdfgimx
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 6 types, 6 molecules jklnop
+Gamma carbonic anhydrase ... , 2 types, 2 molecules yz
+Non-polymers , 13 types, 24 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 (open conformation) Type: COMPLEX / Entity ID: #1-#46 / 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 FIELD |
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: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48933 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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