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- PDB-13he: CryoEM structure of AdhE spirosome from Clostridium thermocellum ... -

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Basic information

Entry
Database: PDB / ID: 13he
TitleCryoEM structure of AdhE spirosome from Clostridium thermocellum uncovered by visual proteomics.
ComponentsAldehyde-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / Spirosome / Filament
Function / homology
Function and homology information


butanol dehydrogenase (NAD+) activity / acetaldehyde dehydrogenase (acetylating) activity / methylglyoxal reductase (NADPH) (acetol producing) activity / alcohol metabolic process / carbon utilization / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase (NAD+) activity / 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. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase ...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. / : / Fe-containing alcohol dehydrogenase family, C-terminal / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde-alcohol dehydrogenase
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsAgdanowski, M.P. / Rodriguez, J.A. / Moser, T. / Evans, J.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: bioRxiv / Year: 2026
Title: Visual exoproteomics of during anaerobic biomass-degradation identifies functional spirosomes.
Authors: Matthew P Agdanowski / Matthew J Kensil / Trevor H Moser / Ethan Humm / Yaneli I Guandique / Kayleigh Mason-Chalmers / Tracy Al-Set / Rachel R Ogorzalek Loo / James E Evans / Robert P ...Authors: Matthew P Agdanowski / Matthew J Kensil / Trevor H Moser / Ethan Humm / Yaneli I Guandique / Kayleigh Mason-Chalmers / Tracy Al-Set / Rachel R Ogorzalek Loo / James E Evans / Robert P Gunsalus / Joseph A Loo / Jose A Rodriguez
Abstract: Visual proteomics enables the study of low-abundance proteins and identification of unknown complexes from heterogeneous samples by complementing high-resolution cryogenic electron microscopy (cryoEM) ...Visual proteomics enables the study of low-abundance proteins and identification of unknown complexes from heterogeneous samples by complementing high-resolution cryogenic electron microscopy (cryoEM) with external inputs on protein identity such as mass spectrometry. Using this approach, we interrogated the exoproteome of the anaerobic cellulose-degrading bacterium as it carried out biomass degradation. Mass spectrometry indicated a broad exoproteome composition, including cellulose degrading machinery CelA and CipA. A focus on large exoproteome assemblies revealed abundant protein filaments and pleomorphic vesicular structures. Analysis of the most abundant protein filaments yielded an ∼4 □ resolution native structure that, aided by mass spectrometry, modeling, and structural searching, was found to be the aldehyde-alcohol dehydrogenase (AdhE) spirosome. AdhE contained both NAD and Fe in their expected binding sites and biochemical and structural analyses of enriched spirosome preparations indicated they were functional. Altered NADH solution concentrations triggered conformational changes in the exoproteomic spirosomes, and the constituent AdhE remained capable of ethanol production. Although the basis for functional extracellular spirosome accumulation in live anaerobic cultures remains unclear, their abundance in crude exoproteomes suggests their presence could influence biomass fueled growth.
History
DepositionMay 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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)573,04418
Polymers568,7286
Non-polymers4,31612
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Aldehyde-alcohol dehydrogenase


Mass: 94788.023 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Acetivibrio thermocellus DSM 1313 (bacteria)
References: UniProt: A0A0H3W5U9
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: AdhE spirosome / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Acetivibrio thermocellus DSM 1313 (bacteria)
Buffer solutionpH: 8 / Details: 20mM Tris pH 8.0, 150mM NaCl, 2mM CaCl2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris1
2150 mMsodium chlorideNaCl1
32 mMcalcium chlorideCaCl21
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was obtained from partially-purified extracellular media and contained an array of unidentified species.
Specimen supportDetails: CFlat 1.2/1.3 300 mesh holey carbon Cu support grids were negatively glow discharged for 20 seconds on the sample side.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Formvar Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285.15 K
Details: Vitification was performed on CFlat 1.2/1.3 300 mesh holey carbon grids with copper support.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 500 nm / Nominal defocus min: 100 nm
Image recordingAverage exposure time: 1.03 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4863
Details: Images were recorded as movies consisting of 50 frames over an exposure time of 1.03 seconds, with a total accumulated dose of 48 electrons per Angstrom
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 6.8E-5 µm / Width: 11520 / Height: 88184

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.4.1particle selection
4cryoSPARC4.4.1CTF correctionPatch CTF Estimation
7Coot0.9.8.96model fitting
9cryoSPARC4.4.1initial Euler assignmentAb Initio Reconstruction
10cryoSPARC4.4.1final Euler assignmentHelical Refinement with optimized helical rise and twist
12cryoSPARC4.4.13D reconstructionHelical Refinement, Local Refinement with mask
13PHENIX2.0-5936model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -166.03 ° / Axial rise/subunit: 60.06 Å / Axial symmetry: C1
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95407 / Algorithm: FOURIER SPACE
Details: Overall resolution 4.07 angstrom as estimated by the masked gold-standard FSC = 0.143 criterion in cryoSPARC. Unmasked FSC values are lower, consistent with expected effects of masking." in the details field.
Num. of class averages: 65 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT
Details: A existing structure's (PDB:8UHW) coordinates were relaxed using the Rosetta Fast Relax algorithm and refined against the EM density from cryoSPARC using Phenix and Coot. Histidine residues ...Details: A existing structure's (PDB:8UHW) coordinates were relaxed using the Rosetta Fast Relax algorithm and refined against the EM density from cryoSPARC using Phenix and Coot. Histidine residues coordinate the iron ion; short distances flagged as clashes correspond to metal coordination geometry.
Atomic model buildingPDB-ID: 8UHW

8uhw


Pdb chain-ID: A / Accession code: 8UHW / Chain residue range: 11-869
Details: published structure was fast relaxed and then used as an initial model for model building and refinement
Pdb chain residue range: 11-869 / Source name: PDB / Type: experimental model

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