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Yorodumi- EMDB-33243: Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33243 | ||||||||||||||||||
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Title | Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 2 | ||||||||||||||||||
Map data | N -NQR state 2 | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information riboflavin binding / NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / FAD binding / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding ...riboflavin binding / NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / FAD binding / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Vibrio cholerae O395 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Kishikawa J / Ishikawa M / Masuya T / Murai M / Barquera B / Miyoshi H | ||||||||||||||||||
Funding support | Japan, United States, 5 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structures of Na-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae. Authors: Jun-Ichi Kishikawa / Moe Ishikawa / Takahiro Masuya / Masatoshi Murai / Yuki Kitazumi / Nicole L Butler / Takayuki Kato / Blanca Barquera / Hideto Miyoshi / Abstract: The Na-pumping NADH-ubiquinone oxidoreductase (Na-NQR) couples electron transfer from NADH to ubiquinone with Na-pumping, generating an electrochemical Na gradient that is essential for energy- ...The Na-pumping NADH-ubiquinone oxidoreductase (Na-NQR) couples electron transfer from NADH to ubiquinone with Na-pumping, generating an electrochemical Na gradient that is essential for energy-consuming reactions in bacteria. Since Na-NQR is exclusively found in prokaryotes, it is a promising target for highly selective antibiotics. However, the molecular mechanism of inhibition is not well-understood for lack of the atomic structural information about an inhibitor-bound state. Here we present cryo-electron microscopy structures of Na-NQR from Vibrio cholerae with or without a bound inhibitor at 2.5- to 3.1-Å resolution. The structures reveal the arrangement of all six redox cofactors including a herein identified 2Fe-2S cluster located between the NqrD and NqrE subunits. A large part of the hydrophilic NqrF is barely visible in the density map, suggesting a high degree of flexibility. This flexibility may be responsible to reducing the long distance between the 2Fe-2S centers in NqrF and NqrD/E. Two different types of specific inhibitors bind to the N-terminal region of NqrB, which is disordered in the absence of inhibitors. The present study provides a foundation for understanding the function of Na-NQR and the binding manner of specific inhibitors. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33243.map.gz | 118.2 MB | EMDB map data format | |
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Header (meta data) | emd-33243-v30.xml emd-33243.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33243_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_33243.png | 126.6 KB | ||
Masks | emd_33243_msk_1.map | 125 MB | Mask map | |
Others | emd_33243_half_map_1.map.gz emd_33243_half_map_2.map.gz | 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33243 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33243 | HTTPS FTP |
-Validation report
Summary document | emd_33243_validation.pdf.gz | 909 KB | Display | EMDB validaton report |
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Full document | emd_33243_full_validation.pdf.gz | 908.6 KB | Display | |
Data in XML | emd_33243_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_33243_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33243 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33243 | HTTPS FTP |
-Related structure data
Related structure data | 7xk4MC 7xk3C 7xk5C 7xk6C 7xk7C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33243.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | N -NQR state 2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33243_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: N -NQR state 2, half map 1
File | emd_33243_half_map_1.map | ||||||||||||
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Annotation | N -NQR state 2, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: N -NQR state 2, half map 2
File | emd_33243_half_map_2.map | ||||||||||||
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Annotation | N -NQR state 2, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, ...
+Supramolecule #1: Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, ...
+Macromolecule #1: Na(+)-translocating NADH-quinone reductase subunit A
+Macromolecule #2: Na(+)-translocating NADH-quinone reductase subunit B
+Macromolecule #3: Na(+)-translocating NADH-quinone reductase subunit C
+Macromolecule #4: Na(+)-translocating NADH-quinone reductase subunit D
+Macromolecule #5: Na(+)-translocating NADH-quinone reductase subunit E
+Macromolecule #6: Na(+)-translocating NADH-quinone reductase subunit F
+Macromolecule #7: FLAVIN MONONUCLEOTIDE
+Macromolecule #8: RIBOFLAVIN
+Macromolecule #9: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #10: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #11: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #12: CALCIUM ION
+Macromolecule #13: FLAVIN-ADENINE DINUCLEOTIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 11 mg/mL | ||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9027 / Average exposure time: 6.5 sec. / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0039 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |