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- EMDB-58600: Cryo-EM map of the acetyl-CoA decarbonylase/synthase (ACDS) compl... -

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Entry
Database: EMDB / ID: EMD-58600
TitleCryo-EM map of the acetyl-CoA decarbonylase/synthase (ACDS) complex from Methanosarcina acetivorans
Map dataAcetyl-CoA decarbonylase/synthase (ACDS) isoform Cdh2 from Methanosarcina acetivorans
Sample
  • Complex: Acetyl-CoA decarbonylase/synthase (ACDS) enzyme complex, isoform Cdh2
    • Complex: CO dehydrogenase (CODH)
      • Protein or peptide: CdhA2
      • Protein or peptide: CdhB2
    • Complex: Acetyl-CoA synthase (ACS)
      • Protein or peptide: CdhC2
    • Complex: Corrinoid iron-sulfur protein (CoFeSP)
      • Protein or peptide: CdhD2
      • Protein or peptide: CdhE2
Keywordsmethanogenesis / acetyl-CoA / anaerobic metabolism / CO dehydrogenase / METAL BINDING PROTEIN
Function / homology
Function and homology information


5-methyltetrahydrosarcinapterin-corrinoid/iron-sulfur protein Co-methyltransferase / methanogenesis, from acetate / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / acetyl-CoA catabolic process / nitric oxide catabolic process / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process ...5-methyltetrahydrosarcinapterin-corrinoid/iron-sulfur protein Co-methyltransferase / methanogenesis, from acetate / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / acetyl-CoA catabolic process / nitric oxide catabolic process / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / acetyltransferase activity / nickel cation binding / iron-sulfur cluster binding / one-carbon metabolic process / methyltransferase activity / response to hydrogen peroxide / peroxidase activity / 4 iron, 4 sulfur cluster binding / methylation / iron ion binding
Similarity search - Function
Acetyl-CoA decarbonylase/synthase complex, gamma subunit, archaea / CO dehydrogenase/acetyl-CoA synthase delta subunit / Acetyl-CoA decarbonylase/synthase complex subunit beta, archaeal / Acetyl-CoA decarbonylase/synthase complex, gamma subunit / Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel / : / CO dehydrogenase/acetyl-CoA synthase delta subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit ...Acetyl-CoA decarbonylase/synthase complex, gamma subunit, archaea / CO dehydrogenase/acetyl-CoA synthase delta subunit / Acetyl-CoA decarbonylase/synthase complex subunit beta, archaeal / Acetyl-CoA decarbonylase/synthase complex, gamma subunit / Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel / : / CO dehydrogenase/acetyl-CoA synthase delta subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Dihydropteroate synthase-like / 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
Acetyl-CoA decarbonylase/synthase complex subunit gamma / Acetyl-CoA decarbonylase/synthase complex subunit delta 2 / Acetyl-CoA decarbonylase/synthase complex subunit beta 2 / Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2 / Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.59 Å
AuthorsZimmer E / Reif-Trauttmansdorff T / Schuller JM
Funding supportEuropean Union, Germany, 2 items
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, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58600.png

Downloads & links

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Map

FileDownload / File: emd_58600.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcetyl-CoA decarbonylase/synthase (ACDS) isoform Cdh2 from Methanosarcina acetivorans
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 550 pix.
= 467.5 Å		0.85 Å/pix.
x 550 pix.
= 467.5 Å		0.85 Å/pix.
x 550 pix.
= 467.5 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.053854328 - 0.13674596
Average (Standard dev.)0.0013396967 (±0.010341318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 467.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58600_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_58600_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_58600_half_map_2.map
Projections & Slices
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Sample components

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Entire : Acetyl-CoA decarbonylase/synthase (ACDS) enzyme complex, isoform Cdh2

EntireName: Acetyl-CoA decarbonylase/synthase (ACDS) enzyme complex, isoform Cdh2
Components
  • Complex: Acetyl-CoA decarbonylase/synthase (ACDS) enzyme complex, isoform Cdh2
    • Complex: CO dehydrogenase (CODH)
      • Protein or peptide: CdhA2
      • Protein or peptide: CdhB2
    • Complex: Acetyl-CoA synthase (ACS)
      • Protein or peptide: CdhC2
    • Complex: Corrinoid iron-sulfur protein (CoFeSP)
      • Protein or peptide: CdhD2
      • Protein or peptide: CdhE2

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Supramolecule #1: Acetyl-CoA decarbonylase/synthase (ACDS) enzyme complex, isoform Cdh2

SupramoleculeName: Acetyl-CoA decarbonylase/synthase (ACDS) enzyme complex, isoform Cdh2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31
Molecular weightTheoretical: 98 kDa/nm

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Supramolecule #2: CO dehydrogenase (CODH)

SupramoleculeName: CO dehydrogenase (CODH) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31

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Supramolecule #3: Acetyl-CoA synthase (ACS)

SupramoleculeName: Acetyl-CoA synthase (ACS) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31

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Supramolecule #4: Corrinoid iron-sulfur protein (CoFeSP)

SupramoleculeName: Corrinoid iron-sulfur protein (CoFeSP) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31

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Macromolecule #1: CdhA2

MacromoleculeName: CdhA2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31
SequenceString: MSKLTTGSFS IEDLESVQIT INNIVGAAKE AAEEKAKELG PMGPTAMAGL ASYRSWNLLL LDRYEPVLTP MCDQCCYCTY GPCDLSGNKR GACGIDMAGQ TGREFFLRVI TGTACHAAHG RHLLDHVIEV FGEDLPLNLG ESNVLTPNVT ICTGLSPKTL GECRAPMEYV ...String:
MSKLTTGSFS IEDLESVQIT INNIVGAAKE AAEEKAKELG PMGPTAMAGL ASYRSWNLLL LDRYEPVLTP MCDQCCYCTY GPCDLSGNKR GACGIDMAGQ TGREFFLRVI TGTACHAAHG RHLLDHVIEV FGEDLPLNLG ESNVLTPNVT ICTGLSPKTL GECRAPMEYV EEQLTQLLAT IHAGQESAEI DYDSKALFSG SLDHVGMEVS DIAQVSAYDF PKADPEAPLI EIGMGSIDKS KPLIVAIGHN VAGVTYIMDY MEENNLTDKM EIAGLCCTAF DMTRYKEADR RAPYAKIVGS LAKELKVIRS GMPDVIVVDE QCVRGDVLSE SQKLKIPVIA SNEKIMMGLP DRTDADVDSI VEEIKSGAIP GCVMLDYDKL GELIPKIAEV MAPIRDAEGI TAIPTDEEFK VYIDKCVKCG ECMLACPEEL DIPEALEYAA KGSYEYLEAL HDVCIGCRRC EQVCKKEIPI LNVLEKAAQK SISEEKGWVR SGRGQASDAE IRKEGLNLVM GTTPGIIAII GCPNYPAGTK DVYLIAEEFL KRNYLLAVSG CSAMDIGMFK DEDGKTLYEK YPGTFAGGGL LNTGSCVSNA HISGAAEKVA GIFAQRTLAG NLAEIADYTL NRVGACGLAW GAYSQKAASI GTGCNIYGIP AVLGPHSSKY RRALIAKNYD ESKWKVYDGR DGSEMTIPPA PEFLLTTAET WQEAIPMMAK ACIRPSDNNM GRSIKLTHWM ELSKKYLGVE PEDWWKFVRN EADLPLAKRE ELLKRLEAEH GWEIDWKRKK IISGPKIKFD VSAQPTNLKR LCKEA

UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2

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Macromolecule #2: CdhB2

MacromoleculeName: CdhB2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31
SequenceString:
MVDTTKNTKL FTSYGVTTSK TTTPEIAAKL ISKAKRPLLV VGTKVLDPEL LDRAVKIAQK ANIPIAATGS SMPGFVGKDV DAKYINLHQL GFYVTDPNWP GLDGNGTYDT LIVLGHIKYY INQVLSGTKN FSTVKAIAIE RNYIQNATMS FGNLSKADHY AALDELIDAL

UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2

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Macromolecule #3: CdhC2

MacromoleculeName: CdhC2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31
SequenceString: MAEFPFEISP MFEGERVRKE GMFVELGGPK SLGLELVRAK PMDEIEDDKV TIVGPDLKEM EEGKTYPWAM IFNIGGELVE PDLESVVERR VHDFINYCQG IMHLNQRYDV WMRVSKDTAA KMDSFEPFGQ AVMMLFKTEL PFIEKMQVTF YTEQAEVEKQ LEEAKAIFKA ...String:
MAEFPFEISP MFEGERVRKE GMFVELGGPK SLGLELVRAK PMDEIEDDKV TIVGPDLKEM EEGKTYPWAM IFNIGGELVE PDLESVVERR VHDFINYCQG IMHLNQRYDV WMRVSKDTAA KMDSFEPFGQ AVMMLFKTEL PFIEKMQVTF YTEQAEVEKQ LEEAKAIFKA RDERTKDLHD EDVDVFYGCT LCQSFAPTNV CVVSPDRVSL CGAINWFDGR AAAKVDPEGP QFEITKGDLI DAEKGEYTGV NDIAKKLSAG EFDKIKLHSF FDAPHTSCGC FEVVGFYIPE VDGIGWVNRE YQGMAPNGIG FSTMAGQTGG GKQIVGFLGI GINYFYSPKF IQADGGWNRV VWLPSMLKDK IAETIPEDLK DKIATENDAT DIESLKAFLQ EKGHPVVATW AAAEEEEEEE EEEEEEVAVA AAPMMMPAAG FQMPAMPMMS GGSSGGIKLT FKNAKITIDK MIISEKKEKK

UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit beta 2

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Macromolecule #4: CdhD2

MacromoleculeName: CdhD2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31
SequenceString: MAKKMKLSDI TNMFAGMDVE ALEGVTIEGD IEIDLGGLGG GFDPMLAAAL GQESAILAQH FARLAGMFGY PVGIGAPAAP AVSPALAAPK LKDLIPAKFD VANIAEWATE IQEVPIGNTS ADGGSRGKRV MLGGEKALPF YFDAPMPNRN QVTIDVFDMR IGLAKAVKEN ...String:
MAKKMKLSDI TNMFAGMDVE ALEGVTIEGD IEIDLGGLGG GFDPMLAAAL GQESAILAQH FARLAGMFGY PVGIGAPAAP AVSPALAAPK LKDLIPAKFD VANIAEWATE IQEVPIGNTS ADGGSRGKRV MLGGEKALPF YFDAPMPNRN QVTIDVFDMR IGLAKAVKEN YDEVMDSPGE WAKKNVEKFN ADMITIHLIS TDPLIKDTPA KEAAKTVEEV LQAVDVPIAI GGSGNPQKDP EVLARAAEVS EGERCLLASA SLNLDYAAIA EAALKYDHDV LSWTQLDMNA QKELNRKLMK QCNVPRDRII MDPTTAALGY GLDYAYTNME RIRLAALMGD DELTFPMSSG TTNAWGARES WMVSSPLKED SDWGPREYRG PIWEIVTGLS LAIAGNDLFM MMHPTSVAVL KQITQTLFGM IDTEQVDVAN WIGAEV

UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit delta 2

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Macromolecule #5: CdhE2

MacromoleculeName: CdhE2 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea) / Strain: MCD31
SequenceString: MKINSPLEAY KYLPQTNCGE CGEATCMAFA SKLIDRSGKT SDCPPLIKEK KFAKKLAELD RLLAPEIRQV TIGVGEKAVN IGGDDVLYRH KLTFFNKTKM FFDVADNMDE AALVERVNSI ANFRKFYVGR NLLLDGVAIR AVSNDPAKFA AAVKKVAEAG LPMIFCSFNP ...String:
MKINSPLEAY KYLPQTNCGE CGEATCMAFA SKLIDRSGKT SDCPPLIKEK KFAKKLAELD RLLAPEIRQV TIGVGEKAVN IGGDDVLYRH KLTFFNKTKM FFDVADNMDE AALVERVNSI ANFRKFYVGR NLLLDGVAIR AVSNDPAKFA AAVKKVAEAG LPMIFCSFNP AVLKAGLEAA KDLKPLLYAA NKDNWKEVGE LAIEYKVPVV VSAFNDLDAL KTLAKTYAEA GIKDIVLDPG TYPTGKGLKD TFTNFLKIRR AGIMGDTEIA YPIMALPFTA WMAGIADPVS ASYWETVMAS VFTIRYGDIM ILHSLEPYAT LPEVHLAETI YTDPRTPVSV DGGMYKVGSP TADSPVLFTT NFALTYYTVE SDISSNGIDC WLLAVDTDGI GVEAAVAGGQ LTADKVKDAF DKAGFDLKTA VNHNTVVTPG LAARLQGDLE DKLGANVKVG PMDSGRIPGW MEKNWPPK

UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit gamma

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
50.0 mMKH2PO4potassium dihydrogen phosphate
150.0 mMNaClsodium chloride

Details: buffer was anaerobised
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blotted with blot force 4 for 4 s.
Detailscrosslinked with 1 mM BS3; addition of 0.04 % (w/v) n-Octyl-beta-D-glucopyranoside

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 19.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 20624
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER

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