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Yorodumi- PDB-7aqq: Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aqq | ||||||
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Title | Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) | ||||||
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 / 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 / ubiquinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / response to salt stress / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / carbonate dehydratase activity / mitochondrial membrane / aerobic respiration / 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 | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å | ||||||
Authors | Klusch, N. / Kuehlbrandt, 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 | 7aqq.cif.gz | 542.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aqq.ent.gz | 438.1 KB | Display | PDB format |
PDBx/mmJSON format | 7aqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aqq_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7aqq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7aqq_validation.xml.gz | 101.6 KB | Display | |
Data in CIF | 7aqq_validation.cif.gz | 149.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aqq ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aqq | 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 (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
#1: Protein | Mass: 13941.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) 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) Arabidopsis thaliana (thale cress) 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) Arabidopsis thaliana (thale cress) 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) Arabidopsis thaliana (thale cress) 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) Arabidopsis thaliana (thale cress) 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) Arabidopsis thaliana (thale cress) 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) Arabidopsis thaliana (thale cress) / References: UniProt: A0A2P2CLH7 |
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#9: Protein | Mass: 11985.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LGE7 |
#10: Protein | Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8RWA7 |
#11: Protein | Mass: 7349.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C9Z5 |
#14: Protein | Mass: 9914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LZI6 |
-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) Arabidopsis thaliana (thale cress) / References: UniProt: A0A384LA38 |
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#12: Protein | Mass: 6810.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZPY5 |
#13: Protein | Mass: 9220.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94AL6 |
#15: Protein | Mass: 11355.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q84W12 |
#16: Protein | Mass: 11808.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178W1I8 |
#18: Protein | Mass: 11965.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZUX4 |
#19: Protein | Mass: 27985.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SMN1 |
-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) Arabidopsis thaliana (thale cress) |
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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) Arabidopsis thaliana (thale cress) 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) Arabidopsis thaliana (thale cress) References: UniProt: Q9FWR5, Lyases; Carbon-oxygen lyases; Hydro-lyases |
-Non-polymers , 9 types, 10 molecules
#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 |
-Sample preparation
Component | Name: Arabidopsis complex I - membrane core / Type: COMPLEX / Entity ID: #1-#21 / 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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459177 / Symmetry type: POINT | ||||||||||||||||||||||||
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