+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11879 | |||||||||
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Title | Cryo-EM structure of Polytomella Complex-I (peripheral arm) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex-I / ELECTRON TRANSPORT | |||||||||
Biological species | Polytomella sp. Pringsheim 198.80 (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
Authors | Klusch N / Kuehlbrandt W | |||||||||
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_11879.map.gz | 45.7 MB | EMDB map data format | |
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Header (meta data) | emd-11879-v30.xml emd-11879.xml | 30.1 KB 30.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11879_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_11879.png | 117 KB | ||
Filedesc metadata | emd-11879.cif.gz | 8.4 KB | ||
Others | emd_11879_half_map_1.map.gz emd_11879_half_map_2.map.gz | 547.6 MB 547.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11879 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11879 | HTTPS FTP |
-Validation report
Summary document | emd_11879_validation.pdf.gz | 783 KB | Display | EMDB validaton report |
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Full document | emd_11879_full_validation.pdf.gz | 782.5 KB | Display | |
Data in XML | emd_11879_validation.xml.gz | 28 KB | Display | |
Data in CIF | emd_11879_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11879 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11879 | HTTPS FTP |
-Related structure data
Related structure data | 7arcMC 7aqqC 7aqrC 7aqwC 7ar7C 7ar8C 7ar9C 7arbC 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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-Map
File | Download / File: emd_11879.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
-Half map: #2
File | emd_11879_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11879_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Polytomella complex I - Peripheral arm
+Supramolecule #1: Polytomella complex I - Peripheral arm
+Macromolecule #1: PSST
+Macromolecule #2: ND9
+Macromolecule #3: ND7
+Macromolecule #4: 24 kDa
+Macromolecule #5: 51 kDa
+Macromolecule #6: 75 kDa
+Macromolecule #7: TYKY
+Macromolecule #8: 39 kDa
+Macromolecule #9: 18 kDa
+Macromolecule #10: 13 kDa
+Macromolecule #11: B8
+Macromolecule #12: SDAP2
+Macromolecule #13: B13
+Macromolecule #14: B14
+Macromolecule #15: B17.2
+Macromolecule #16: B14.5a
+Macromolecule #17: IRON/SULFUR CLUSTER
+Macromolecule #18: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #19: FLAVIN MONONUCLEOTIDE
+Macromolecule #20: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #21: ZINC ION
+Macromolecule #22: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #23: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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: 64.0 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 |