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Yorodumi- EMDB-55749: Local refinement of E. coli Complex I WT membrane domain in LMNG -
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Open data
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Basic information
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| Title | Local refinement of E. coli Complex I WT membrane domain in LMNG | |||||||||
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Keywords | PROTON TRANSPORT / bioenergetics | |||||||||
| Function / homology | Function and homology informationNADH dehydrogenase (quinone) (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport ...NADH dehydrogenase (quinone) (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Kovalova T / Beghiah A / Kaila VRI | |||||||||
| Funding support | Sweden, 2 items
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Citation | Journal: Nat Commun / Year: 2026Title: A carboxylate switch point controls long-range energy transduction in respiratory Complex I. Authors: Adel Beghiah / Patricia Saura / Terezia Kovalova / Franziska Hoeser / Thorsten Friedrich / Ville R I Kaila / ![]() Abstract: Complex I is a highly intricate membrane-bound protein complex that powers the cellular energy metabolism by a long-range ( > 300 Å) proton-coupled electron transfer (PCET) reaction. Here, we ...Complex I is a highly intricate membrane-bound protein complex that powers the cellular energy metabolism by a long-range ( > 300 Å) proton-coupled electron transfer (PCET) reaction. Here, we investigate the highly debated coupling mechanism of Complex I by probing the charge transfer reaction along its functionally central carboxylate pathway (E-channel). By combining biophysical and site-directed mutagenesis experiments with high-resolution (2.6-2.8 Å) cryo-electron microscopy (cryo-EM) and multiscale simulations, we identify a conserved carboxylate switch point (D79) that mediates proton transfer by establishing a kinetic gate and couples the redox chemistry to proton pumping. We find that mutation of the identified site, as found in patients suffering from severe neurodegenerative disorders, drastically perturbs the charge transfer mechanism, and results in a 20% PCET activity. Our combined findings illustrate mechanistic principles of molecular gates underlying long-range charge transfer reactions, and show how disease mutations perturb the function of conserved switch points in energy transduction. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_55749.map.gz | 683.6 MB | EMDB map data format | |
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| Header (meta data) | emd-55749-v30.xml emd-55749.xml | 32.5 KB 32.5 KB | Display Display | EMDB header |
| Images | emd_55749.png | 59.2 KB | ||
| Masks | emd_55749_msk_1.map | 1.3 GB | Mask map | |
| Filedesc metadata | emd-55749.cif.gz | 8.5 KB | ||
| Others | emd_55749_additional_1.map.gz emd_55749_half_map_1.map.gz emd_55749_half_map_2.map.gz | 1.3 GB 1.2 GB 1.2 GB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-55749 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-55749 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9takMC ![]() 9tajC ![]() 9talC ![]() 9tamC ![]() 9tanC ![]() 9taoC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_55749.map.gz / Format: CCP4 / Size: 1.3 GB / 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: 0.825 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_55749_msk_1.map | ||||||||||||
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-Additional map: #1
| File | emd_55749_additional_1.map | ||||||||||||
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-Half map: #1
| File | emd_55749_half_map_1.map | ||||||||||||
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-Half map: #2
| File | emd_55749_half_map_2.map | ||||||||||||
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Sample components
+Entire : NADH-quinone oxidoreductase, Complex I
+Supramolecule #1: NADH-quinone oxidoreductase, Complex I
+Macromolecule #1: NADH-quinone oxidoreductase subunit H
+Macromolecule #2: NADH-quinone oxidoreductase subunit J
+Macromolecule #3: NADH-quinone oxidoreductase subunit K
+Macromolecule #4: NADH-quinone oxidoreductase subunit M
+Macromolecule #5: NADH-quinone oxidoreductase subunit A
+Macromolecule #6: NADH-quinone oxidoreductase subunit B
+Macromolecule #7: NADH-quinone oxidoreductase subunit L
+Macromolecule #8: NADH-quinone oxidoreductase subunit N
+Macromolecule #9: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #10: EICOSANE
+Macromolecule #11: CARDIOLIPIN
+Macromolecule #12: TRIDECANE
+Macromolecule #13: Ubiquinone-8
+Macromolecule #14: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 4.0 mg/mL |
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| Buffer | pH: 6 |
| Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
Sweden, 2 items
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Processing
FIELD EMISSION GUN
