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Yorodumi- PDB-7aqw: Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane tip) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aqw | ||||||
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Title | Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane tip) | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Complex-I | ||||||
Function / homology | Function and homology information photorespiration / plant-type vacuole / plastid / respiratory chain complex I / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl carrier activity ...photorespiration / plant-type vacuole / plastid / respiratory chain complex I / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / proton transmembrane transport / mitochondrial membrane / electron transport chain / mitochondrial intermembrane space / fatty acid biosynthetic process / carbohydrate metabolic process / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 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 | 7aqw.cif.gz | 299.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aqw.ent.gz | 241 KB | Display | PDB format |
PDBx/mmJSON format | 7aqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aqw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7aqw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7aqw_validation.xml.gz | 68.6 KB | Display | |
Data in CIF | 7aqw_validation.cif.gz | 100.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aqw ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aqw | HTTPS FTP |
-Related structure data
Related structure data | 11874MC 7aqqC 7aqrC 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 ... , 2 types, 2 molecules LM
#1: 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) |
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#2: Protein | Mass: 55995.664 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) |
-Protein , 5 types, 5 molecules Tcgim
#3: Protein | Mass: 13735.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P53665 |
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#4: Protein | Mass: 9876.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VZT9 |
#5: Protein | Mass: 12648.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SLC8 |
#6: 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 |
#10: Protein | Mass: 8305.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178VZI4 |
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 6 types, 6 molecules jklnop
#7: Protein | Mass: 7582.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LDK3 |
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#8: Protein | Mass: 8064.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O64725 |
#9: Protein | Mass: 13225.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FGK0 |
#11: Protein | Mass: 13638.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q945M1 |
#12: Protein | Mass: 11757.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SKC9 |
#13: Protein | Mass: 12462.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94C12 |
-Non-polymers , 3 types, 3 molecules
#14: Chemical | ChemComp-PTY / |
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#15: Chemical | ChemComp-PC7 / ( |
#16: Chemical | ChemComp-8Q1 / |
-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 tip / Type: COMPLEX / Entity ID: #1-#13 / 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: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459177 / Symmetry type: POINT | ||||||||||||||||||||||||
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