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- PDB-31ox: Cryo-EM structure of the CO dehydrogenase (CODH) subcomplex from ... -

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Basic information

Entry
Database: PDB / ID: 31ox
TitleCryo-EM structure of the CO dehydrogenase (CODH) subcomplex from Methanosarcina acetivorans
Components
  • Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
  • Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
KeywordsMETAL BINDING PROTEIN / methanogenesis / acetyl-CoA / anaerobic metabolism / CO dehydrogenase
Function / homology
Function and homology information


methanogenesis, from acetate / nitric oxide catabolic process / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / nickel cation binding / response to hydrogen peroxide / peroxidase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / DHS-like NAD/FAD-binding domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. ...Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / DHS-like NAD/FAD-binding domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Fe(3)-Ni(1)-S(4) cluster / IRON/SULFUR CLUSTER / Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2 / Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsZimmer, E. / Reif-Trauttmansdorff, T. / Schuller, J.M.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101075992European Union
German Research Foundation (DFG)RTG 2937 Germany
CitationJournal: bioRxiv / Year: 2026
Title: Interface swapping orchestrates carbon transfer in the archaeal acetyl-CoA decarbonylase/synthase.
Authors: Erik Zimmer / Tristan Reif-Trauttmansdorff / Anthony Ciancone / Sofia Appelgren / Jörg Kahnt / Darja Deobald / Frank Abendroth / Olalla Vázquez / Georg K A Hochberg / Francis J O'Reilly / Jan M Schuller /
Abstract: The Wood-Ljungdahl pathway is one of biology's most ancient routes for carbon fixation and energy metabolism, used by organisms such as methanogenic archaea. One of its central metabolic complexes is ...The Wood-Ljungdahl pathway is one of biology's most ancient routes for carbon fixation and energy metabolism, used by organisms such as methanogenic archaea. One of its central metabolic complexes is the acetyl-CoA decarbonylase/synthase (ACDS) complex, catalyzing acetyl-CoA synthesis and cleavage through the coordinated action of carbon monoxide dehydrogenase (CODH), acetyl-CoA synthase (ACS), and corrinoid iron-sulfur protein (CoFeSP). Unlike bacterial CODH/ACS, archaeal ACDS lacks a stable bifunctional CODH-ACS architecture, raising the question of how reactive CO and methyl intermediates are efficiently transferred between catalytic modules. Using cryo-electron microscopy, crosslinking mass spectrometry, small-angle X-ray scattering, and biophysical analyses, we resolved the organization and dynamics of the ~2 MDa archaeal ACDS supercomplex from . We identified CoFeSP as a central architectural scaffold that self-assembles into hexa- to octameric oligomers via a conserved N-terminal region of the CdhD subunit. This scaffold likely tethers CODH and ACS through conserved disordered terminal regions, positioning the catalytic modules in the complex's periphery. We propose a mechanism in which ACS transiently alternates between CODH and CoFeSP, enabling efficient CO and methyl-group transfer without stable binary complexes. This dynamic organization represents a fundamental difference to the stable bifunctional CODH/ACS in bacteria, highlighting how transient interactions enable efficient acetyl-CoA metabolism in archaea.
History
DepositionJun 16, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 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

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Assembly

Deposited unit
2: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
3: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
C: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
D: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,36713
Polymers213,0854
Non-polymers3,2829
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, gel filtration, mass spectrometry, cross-linking, homology, assay for oligomerization, mass photometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2 / ACDS complex subunit epsilon 2 / ACDS complex carbon monoxide dehydrogenase subunit epsilon 2 / ...ACDS complex subunit epsilon 2 / ACDS complex carbon monoxide dehydrogenase subunit epsilon 2 / ACDS CODH subunit epsilon 2


Mass: 18487.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / Strain: MCD31 / References: UniProt: Q8TJC5
#2: Protein Acetyl-CoA decarbonylase/synthase complex subunit alpha 2 / ACDS complex subunit alpha 2 / ACDS complex carbon monoxide dehydrogenase subunit alpha 2 / ACDS ...ACDS complex subunit alpha 2 / ACDS complex carbon monoxide dehydrogenase subunit alpha 2 / ACDS CODH subunit alpha 2


Mass: 88055.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / Strain: MCD31
References: UniProt: Q8TJC6, anaerobic carbon monoxide dehydrogenase
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-RQM / Fe(3)-Ni(1)-S(4) cluster


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: CO dehydrogenase (CODH) isoform Cdh2 / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.213 MDaYES
21213 kDa/nmYES
3152 kDa/nmYES
4198 kDa/nmYES
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31
Buffer solutionpH: 7.2 / Details: buffer was anaerobised
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMpotassium dihydrogen phosphateKH2PO41
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: crosslinked with 1 mM BS3; addition of 0.04 % (w/v) n-Octyl-beta-D-glucopyranoside
Specimen supportDetails: QUANTIFOIL R 1.2/1.3 copper grids were glow discharged for 25 s with a current of 15 mA in a PELCO easiGlow device (Ted Pella).
Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blotted with blot force 4 for 4 s

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5987

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
4cryoSPARC4CTF correction
7Coot0.9.8.96model fitting
12cryoSPARC53D reconstruction
13PHENIX2.0_5936model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 371631
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187510 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 24.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002214549
ELECTRON MICROSCOPYf_angle_d0.651719774
ELECTRON MICROSCOPYf_chiral_restr0.03922236
ELECTRON MICROSCOPYf_plane_restr0.00352504
ELECTRON MICROSCOPYf_dihedral_angle_d3.91511985

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