[English] 日本語
Yorodumi- EMDB-11872: Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11872 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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) / Mouse-ear cress (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Klusch N / Kuehlbrandt W / Yildiz O | |||||||||
Funding support | Germany, 1 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11872.map.gz | 40.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11872-v30.xml emd-11872.xml | 35.7 KB 35.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11872_fsc.xml | 21.3 KB | Display | FSC data file |
Images | emd_11872.png | 141.2 KB | ||
Others | emd_11872_half_map_1.map.gz emd_11872_half_map_2.map.gz | 631.2 MB 631.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11872 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11872 | HTTPS FTP |
-Related structure data
Related structure data | 7aqqMC 7aqrC 7aqwC 7ar7C 7ar8C 7ar9C 7arbC 7arcC 7ardC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11872.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: #2
File | emd_11872_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_11872_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Arabidopsis complex I - membrane core
+Supramolecule #1: Arabidopsis complex I - membrane core
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #3: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #4: NADH dehydrogenase subunit 4L
+Macromolecule #5: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #6: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #7: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #8: AT3G07480.1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
+Macromolecule #10: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
+Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #12: At2g46540/F11C10.23
+Macromolecule #13: Excitatory amino acid transporter
+Macromolecule #14: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
+Macromolecule #15: At4g16450
+Macromolecule #16: P1
+Macromolecule #17: unknown
+Macromolecule #18: Uncharacterized protein At2g27730, mitochondrial
+Macromolecule #19: Gamma carbonic anhydrase-like 2, mitochondrial
+Macromolecule #20: Gamma carbonic anhydrase 2, mitochondrial
+Macromolecule #21: Gamma carbonic anhydrase 1, mitochondrial
+Macromolecule #22: Ubiquinone-9
+Macromolecule #23: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #24: Lauryl Maltose Neopentyl Glycol
+Macromolecule #25: FE (III) ION
+Macromolecule #26: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...
+Macromolecule #27: ZINC ION
+Macromolecule #28: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #29: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
+Macromolecule #30: Phosphatidylinositol
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |