|Entry||Database: PDB / ID: 6nbb|
|Title||Horse liver alcohol dehydrogenase determined using single-particle cryo-EM at 200 keV|
|Components||Alcohol dehydrogenase E chain|
|Keywords||OXIDOREDUCTASE / dehydrogenase / NADH-binding / homo-2-mer|
|Function / homology||GroES-like superfamily / Alcohol dehydrogenase, C-terminal / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase GroES-like domain / Zinc-binding dehydrogenase / NAD(P)-binding domain superfamily / Polyketide synthase, enoylreductase domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase, zinc-type, conserved site / alcohol dehydrogenase activity, zinc-dependent ...GroES-like superfamily / Alcohol dehydrogenase, C-terminal / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase GroES-like domain / Zinc-binding dehydrogenase / NAD(P)-binding domain superfamily / Polyketide synthase, enoylreductase domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase, zinc-type, conserved site / alcohol dehydrogenase activity, zinc-dependent / alcohol dehydrogenase / ethanol oxidation / retinol dehydrogenase activity / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol / Alcohol dehydrogenase E chain|
Function and homology information
|Specimen source||Equus caballus (horse)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.9 Å resolution|
|Authors||Herzik Jr., M.A. / Wu, M. / Lander, G.C.|
|Citation||Journal: Nat Commun / Year: 2019|
Title: High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM.
Authors: Mark A Herzik / Mengyu Wu / Gabriel C Lander
SummaryFull reportAbout validation report
|Date||Deposition: Dec 6, 2018 / Release: Mar 13, 2019|
|Structure viewer||Molecule: |
Downloads & links
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
|Number of models||10|
Mass: 39853.273 Da / Num. of mol.: 2 / Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: P00327, alcohol dehydrogenase
Mass: 663.425 Da / Num. of mol.: 2 / Formula: C21H27N7O14P2 / Nicotinamide adenine dinucleotide / Comment: NAD *YM
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: Alcohol dehydrogenase from equine liver / Type: COMPLEX|
Details: Lyophilized horse liver ADH purchased from Sigma Aldrich was further purified to homogeneity.
Entity ID: 1 / Source: RECOMBINANT
|Molecular weight||Value: 0.081 MDa / Experimental value: NO|
|Source (natural)||Organism: Equus caballus (horse)|
|Source (recombinant)||Organism: Escherichia coli (E. coli)|
|Buffer solution||pH: 8.5|
|Specimen||Conc.: 2.5 mg/ml|
Details: Lyophilized horse liver ADH (Sigma Aldrich) was solubilized and further purified to homogeneity.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
|Specimen support||Details: Grids were plasma cleaned using a Solarus plasma cleaner (Gatan, Inc.).|
Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 kelvins|
Details: Sample was manually blotted for 4-5 seconds using Whatman No. 1 filter paper immediately prior to plunge-freezing.
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 73000 / Nominal defocus max: 16000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 11 sec. / Electron dose: 69 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 2 / Number of real images: 1151|
|Image scans||Sampling size: 5 microns / Width: 3710 / Height: 3838 / Movie frames/image: 44 / Used frames/image: 1-44|
|Software||Name: PHENIX / Version: 1.11.1_2580: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 1232543|
|Symmetry||Point symmetry: C2|
|3D reconstruction||Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 11672 / Algorithm: BACK PROJECTION / Symmetry type: POINT|
|Atomic model building||Overall b value: 67 / Ref protocol: FLEXIBLE FIT / Ref space: REAL|
|Atomic model building||PDB-ID: 2JHF|
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