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Yorodumi- EMDB-10552: Helical reconstruction of AdhE from Escherichia coli in its exten... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10552 | |||||||||
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Title | Helical reconstruction of AdhE from Escherichia coli in its extended conformation | |||||||||
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Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Fronzes R / Pony P | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Filamentation of the bacterial bi-functional alcohol/aldehyde dehydrogenase AdhE is essential for substrate channeling and enzymatic regulation. Authors: Pauline Pony / Chiara Rapisarda / Laurent Terradot / Esther Marza / Rémi Fronzes / Abstract: Acetaldehyde-alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanol via an acetaldehyde intermediate during ...Acetaldehyde-alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanol via an acetaldehyde intermediate during ethanol fermentation in an anaerobic environment. This two-step reaction is associated to NAD regeneration, essential for glycolysis. The bifunctional AdhE enzyme is conserved in all bacterial kingdoms but also in more phylogenetically distant microorganisms such as green microalgae. It is found as an oligomeric form called spirosomes, for which the function remains elusive. Here, we use cryo-electron microscopy to obtain structures of Escherichia coli spirosomes in different conformational states. We show that spirosomes contain active AdhE monomers, and that AdhE filamentation is essential for its activity in vitro and function in vivo. The detailed analysis of these structures provides insight showing that AdhE filamentation is essential for substrate channeling within the filament and for the regulation of enzyme activity. | |||||||||
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_10552.map.gz | 31 MB | EMDB map data format | |
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Header (meta data) | emd-10552-v30.xml emd-10552.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10552_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_10552.png | 52.8 KB | ||
Others | emd_10552_additional.map.gz emd_10552_additional_1.map.gz emd_10552_half_map_1.map.gz emd_10552_half_map_2.map.gz | 10.5 MB 10.5 MB 31.3 MB 31.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10552 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10552 | HTTPS FTP |
-Validation report
Summary document | emd_10552_validation.pdf.gz | 452.9 KB | Display | EMDB validaton report |
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Full document | emd_10552_full_validation.pdf.gz | 452.1 KB | Display | |
Data in XML | emd_10552_validation.xml.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10552 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10552 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10552.map.gz / Format: CCP4 / Size: 40.6 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: 1.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_10552_additional.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_10552_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10552_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10552_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AdhE dimer in complex with NAD+ and Fe2+
Entire | Name: AdhE dimer in complex with NAD+ and Fe2+ |
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Components |
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-Supramolecule #1: AdhE dimer in complex with NAD+ and Fe2+
Supramolecule | Name: AdhE dimer in complex with NAD+ and Fe2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 0.0025 µm / Calibrated defocus min: 0.0005 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |