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- PDB-8uhw: The structure of the Clostridium thermocellum AdhE spirosome -

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Basic information

Entry
Database: PDB / ID: 8uhw
TitleThe structure of the Clostridium thermocellum AdhE spirosome
ComponentsAldehyde-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde-alcohol dehydrogenase / Complex / Spirosome
Function / homology
Function and homology information


methylglyoxal reductase (NADPH) (acetol producing) activity / butanol dehydrogenase (NAD+) activity / acetaldehyde dehydrogenase (acetylating) activity / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / carbon utilization / metal ion binding / cytosol
Similarity search - Function
Butanol dehydrogenase-like / Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Butanol dehydrogenase-like / Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
: / Aldehyde-alcohol dehydrogenase
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsZiegler, S.J. / Gruber, J.N.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Elife / Year: 2024
Title: Structural characterization and dynamics of AdhE ultrastructures from Clostridium thermocellum: A containment strategy for toxic intermediates
Authors: Ziegler, S. / Knott, B. / Gruber, J. / Hengge, N. / Xu, Q. / Olson, D. / Romero, E. / Joubert, L. / Bomble, Y.
History
DepositionOct 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde-alcohol dehydrogenase
B: Aldehyde-alcohol dehydrogenase
C: Aldehyde-alcohol dehydrogenase
D: Aldehyde-alcohol dehydrogenase
E: Aldehyde-alcohol dehydrogenase
F: Aldehyde-alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)587,91111
Polymers587,6326
Non-polymers2795
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Aldehyde-alcohol dehydrogenase


Mass: 97938.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: adhE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3W5U9
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homo-oligomer complex of AdhE / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Acetivibrio thermocellus DSM 1313 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(HOCH2)3CNH21
2150 mMSodium ChlorideNaCl1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1 / Category: particle selection
CTF correctionType: NONE
Particle selectionNum. of particles selected: 504494
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90912 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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