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Yorodumi- EMDB-11878: Cryo-EM structure of Arabidopsis thaliana Complex-I (complete com... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11878 | |||||||||
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Title | Cryo-EM structure of Arabidopsis thaliana Complex-I (complete composition) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information 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 / regulation of reactive oxygen species metabolic process / response to osmotic stress / plastid / respiratory chain complex I / cobalt ion binding / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / ubiquinone binding / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport / response to salt stress / aerobic respiration / respiratory electron transport chain / chloroplast / mitochondrial membrane / carbonate dehydratase activity / electron transport chain / mitochondrial intermembrane space / transmembrane transport / fatty acid biosynthetic process / 2 iron, 2 sulfur cluster binding / NAD binding / peroxisome / 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 / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / Mouse-ear cress (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||
Authors | Klusch N / Kuelbrandt W / Yildiz O | |||||||||
Funding support | Germany, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11878.map.gz | 20.7 MB | EMDB map data format | |
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Header (meta data) | emd-11878-v30.xml emd-11878.xml | 59.2 KB 59.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11878_fsc.xml | 21.3 KB | Display | FSC data file |
Images | emd_11878.png | 114.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11878 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11878 | HTTPS FTP |
-Validation report
Summary document | emd_11878_validation.pdf.gz | 333.6 KB | Display | EMDB validaton report |
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Full document | emd_11878_full_validation.pdf.gz | 333.2 KB | Display | |
Data in XML | emd_11878_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | emd_11878_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11878 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11878 | HTTPS FTP |
-Related structure data
Related structure data | 7arbMC 7aqqC 7aqrC 7aqwC 7ar7C 7ar8C 7ar9C 7arcC 7ardC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11878.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Cryo-EM structure of Arabidopsis thaliana Complex-I (complete com...
+Supramolecule #1: Cryo-EM structure of Arabidopsis thaliana Complex-I (complete com...
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
+Macromolecule #4: NADH dehydrogenase subunit 7
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH dehydrogenase subunit 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: AT3G07480.1
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #20: Acyl carrier protein 1, mitochondrial
+Macromolecule #21: Acyl carrier protein 2, mitochondrial
+Macromolecule #22: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #27: At2g46540/F11C10.23
+Macromolecule #28: Transmembrane protein
+Macromolecule #29: Excitatory amino acid transporter
+Macromolecule #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
+Macromolecule #31: At4g16450
+Macromolecule #32: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
+Macromolecule #33: P1
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #37: B15 -- 1 beta subcomplex subunit 4
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
+Macromolecule #41: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #42: Furry
+Macromolecule #43: unknown
+Macromolecule #44: Uncharacterized protein At2g27730, mitochondrial
+Macromolecule #45: Gamma carbonic anhydrase-like 2, mitochondrial
+Macromolecule #46: Gamma carbonic anhydrase 2, mitochondrial
+Macromolecule #47: Gamma carbonic anhydrase 1, mitochondrial
+Macromolecule #48: IRON/SULFUR CLUSTER
+Macromolecule #49: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #50: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #51: FLAVIN MONONUCLEOTIDE
+Macromolecule #52: Ubiquinone-9
+Macromolecule #53: Lauryl Maltose Neopentyl Glycol
+Macromolecule #54: FE (III) ION
+Macromolecule #55: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #56: ZINC ION
+Macromolecule #57: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #58: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...
+Macromolecule #59: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #60: Phosphatidylinositol
+Macromolecule #61: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |