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- EMDB-11880: Cryo-EM structure of Polytomella Complex-I (complete composition) -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11880 | |||||||||
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Title | Cryo-EM structure of Polytomella Complex-I (complete composition) | |||||||||
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Function / homology | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex 1 LYR protein domain / ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Klusch N / Kuehlbrandt W / Yildiz O | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 24.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 60.2 KB 60.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21.3 KB | Display | ![]() |
Images | ![]() | 111.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ardMC ![]() 7aqqC ![]() 7aqrC ![]() 7aqwC ![]() 7ar7C ![]() 7ar8C ![]() 7ar9C ![]() 7arbC ![]() 7arcC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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Sample components
+Entire : Cryo-EM structure of Polytomella Complex-I (complete composition)
+Supramolecule #1: Cryo-EM structure of Polytomella Complex-I (complete composition)
+Macromolecule #1: ND3
+Macromolecule #2: PSST
+Macromolecule #3: ND9
+Macromolecule #4: ND7
+Macromolecule #5: 24 kDa
+Macromolecule #6: 51 kDa
+Macromolecule #7: 75 kDa
+Macromolecule #8: ND1
+Macromolecule #9: TYKY
+Macromolecule #10: ND6
+Macromolecule #11: ND4L
+Macromolecule #12: ND5
+Macromolecule #13: ND4
+Macromolecule #14: ND2
+Macromolecule #15: C1-FDX
+Macromolecule #16: 39 kDa
+Macromolecule #17: 18 kDa
+Macromolecule #18: 13 kDa
+Macromolecule #19: B8
+Macromolecule #20: SDAP1
+Macromolecule #21: SDAP2
+Macromolecule #22: B13
+Macromolecule #23: B14
+Macromolecule #24: PGIV
+Macromolecule #25: B14.7
+Macromolecule #26: B16.6
+Macromolecule #27: MWFE
+Macromolecule #28: B9
+Macromolecule #29: KFYI
+Macromolecule #30: B14.5b
+Macromolecule #31: 15 kDa
+Macromolecule #32: MNLL
+Macromolecule #33: ESSS
+Macromolecule #34: NUOP4
+Macromolecule #35: NUOP5
+Macromolecule #36: AGGG
+Macromolecule #37: B12
+Macromolecule #38: ASHI
+Macromolecule #39: B15
+Macromolecule #40: Complex I-B22
+Macromolecule #41: B18
+Macromolecule #42: PDSW
+Macromolecule #43: B17.2
+Macromolecule #44: B14.5a
+Macromolecule #45: NUOP7
+Macromolecule #46: NUOP8
+Macromolecule #47: unknown
+Macromolecule #48: unknown
+Macromolecule #49: CAL
+Macromolecule #50: CA2
+Macromolecule #51: CA3
+Macromolecule #52: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...
+Macromolecule #53: IRON/SULFUR CLUSTER
+Macromolecule #54: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #55: FLAVIN MONONUCLEOTIDE
+Macromolecule #56: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #57: CARDIOLIPIN
+Macromolecule #58: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #59: ZINC ION
+Macromolecule #60: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #61: water
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |