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Yorodumi- EMDB-11876: Cryo-EM structure of Arabidopsis thaliana complex-I (closed confo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11876 | |||||||||
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Title | Cryo-EM structure of Arabidopsis thaliana complex-I (closed conformation) | |||||||||
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 / respiratory chain complex I / ubiquinone-6 biosynthetic process / regulation of reactive oxygen species metabolic process / response to osmotic stress / plastid / cobalt ion binding / NADH:ubiquinone reductase (H+-translocating) / protein homotrimerization / : / mitochondrial electron transport, NADH to ubiquinone / : / chloroplast thylakoid membrane / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / response to salt stress / aerobic respiration / respiratory electron transport chain / chloroplast / mitochondrial membrane / electron transport chain / carbonate dehydratase activity / mitochondrial intermembrane space / transmembrane transport / fatty acid biosynthetic process / 2 iron, 2 sulfur cluster binding / peroxisome / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / carbohydrate metabolic process / mitochondrial matrix / copper ion binding / protein-containing complex 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: 3.53 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_11876.map.gz | 52.2 MB | EMDB map data format | |
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Header (meta data) | emd-11876-v30.xml emd-11876.xml | 63.2 KB 63.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11876_fsc.xml | 21.3 KB | Display | FSC data file |
Images | emd_11876.png | 135.4 KB | ||
Others | emd_11876_half_map_1.map.gz emd_11876_half_map_2.map.gz | 672.5 MB 672.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11876 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11876 | HTTPS FTP |
-Validation report
Summary document | emd_11876_validation.pdf.gz | 455.9 KB | Display | EMDB validaton report |
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Full document | emd_11876_full_validation.pdf.gz | 455.4 KB | Display | |
Data in XML | emd_11876_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | emd_11876_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11876 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11876 | HTTPS FTP |
-Related structure data
Related structure data | 7ar8MC 7aqqC 7aqrC 7aqwC 7ar7C 7ar9C 7arbC 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_11876.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Half map: #2
File | emd_11876_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11876_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of Arabidopsis thaliana complex-I (closed confo...
+Supramolecule #1: Cryo-EM structure of Arabidopsis thaliana complex-I (closed confo...
+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: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #50: FLAVIN MONONUCLEOTIDE
+Macromolecule #51: Ubiquinone-9
+Macromolecule #52: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #53: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...
+Macromolecule #54: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #55: FE (III) ION
+Macromolecule #56: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #57: ZINC ION
+Macromolecule #58: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #59: Lauryl Maltose Neopentyl Glycol
+Macromolecule #60: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
+Macromolecule #61: Phosphatidylinositol
-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 |