+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12654 | |||||||||
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Title | Respiratory complex I from Escherichia coli - conformation 2 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / molybdopterin cofactor binding / cellular respiration / respiratory chain complex I / ubiquinone binding / NADH dehydrogenase activity ...: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / molybdopterin cofactor binding / cellular respiration / respiratory chain complex I / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli B (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Kolata P / Efremov RG | |||||||||
Funding support | Belgium, 1 items
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Citation | Journal: Elife / Year: 2021 Title: Structure of respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation. Authors: Piotr Kolata / Rouslan G Efremov / Abstract: Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I ...Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I from is among the best functionally characterized complexes, but its structure remains unknown, hindering further studies to understand the enzyme coupling mechanism. Here, we describe the single particle cryo-electron microscopy (cryo-EM) structure of the entire catalytically active complex I reconstituted into lipid nanodiscs. The structure of this mesophilic bacterial complex I displays highly dynamic connection between the peripheral and membrane domains. The peripheral domain assembly is stabilized by unique terminal extensions and an insertion loop. The membrane domain structure reveals novel dynamic features. Unusual conformation of the conserved interface between the peripheral and membrane domains suggests an uncoupled conformation of the complex. Considering constraints imposed by the structural data, we suggest a new simple hypothetical coupling mechanism for the molecular machine. | |||||||||
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_12654.map.gz | 56.3 MB | EMDB map data format | |
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Header (meta data) | emd-12654-v30.xml emd-12654.xml | 35.6 KB 35.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12654_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_12654.png | 43.9 KB | ||
Others | emd_12654_half_map_1.map.gz emd_12654_half_map_2.map.gz | 46 MB 46.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12654 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12654 | HTTPS FTP |
-Validation report
Summary document | emd_12654_validation.pdf.gz | 375.9 KB | Display | EMDB validaton report |
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Full document | emd_12654_full_validation.pdf.gz | 375 KB | Display | |
Data in XML | emd_12654_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_12654_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12654 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12654 | HTTPS FTP |
-Related structure data
Related structure data | 7nyuMC 7nyhC 7nyrC 7nyvC 7nz1C C: citing same article (ref.) M: atomic model generated by this map |
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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_12654.map.gz / Format: CCP4 / Size: 59.6 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: 1.542 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_12654_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12654_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Respiratory complex I from Escherichia coli - conformation 2
+Supramolecule #1: Respiratory complex I from Escherichia coli - conformation 2
+Macromolecule #1: NADH-quinone oxidoreductase subunit A
+Macromolecule #2: NADH-quinone oxidoreductase subunit B
+Macromolecule #3: NADH-quinone oxidoreductase subunit C/D
+Macromolecule #4: NADH-quinone oxidoreductase subunit E
+Macromolecule #5: NADH-quinone oxidoreductase subunit F
+Macromolecule #6: NADH-quinone oxidoreductase subunit G
+Macromolecule #7: NADH-quinone oxidoreductase subunit H
+Macromolecule #8: NADH-quinone oxidoreductase subunit I
+Macromolecule #9: NADH-quinone oxidoreductase subunit J
+Macromolecule #10: NADH-quinone oxidoreductase subunit K
+Macromolecule #11: NADH-quinone oxidoreductase subunit L
+Macromolecule #12: NADH-quinone oxidoreductase subunit M
+Macromolecule #13: NADH-quinone oxidoreductase subunit N
+Macromolecule #14: IRON/SULFUR CLUSTER
+Macromolecule #15: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #16: FLAVIN MONONUCLEOTIDE
+Macromolecule #17: CALCIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 6.8 Component:
Details: The buffer was used for gel filtration of protein reconstituted in lipid nanodiscs | ||||||||||||
Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.028 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 97 % / Chamber temperature: 296 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 9122 / Average exposure time: 3.0 sec. / Average electron dose: 64.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.55 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |