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- EMDB-50754: Closed CODH/ACS in the methylated state -

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Basic information

Entry
Database: EMDB / ID: EMD-50754
TitleClosed CODH/ACS in the methylated state
Map datamap locally refined on the asymmetric unit
Sample
  • Complex: CODH/ACS complex
    • Protein or peptide: Carbon monoxide dehydrogenase
    • Protein or peptide: CO-methylating acetyl-CoA synthase
  • Ligand: Fe(3)-Ni(1)-S(4) cluster
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: NICKEL (II) ION
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsCODH / ACS / CO2 fixation / reductive acetyl-CoA pathway / Wood-Ljungdahl pathway / OXIDOREDUCTASE
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / 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 / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria) / Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsRuickoldt J / Wendler P / Dobbek H
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008/1 390540038 Germany
CitationJournal: Nat Catal / Year: 2025
Title: Ligand binding to a Ni-Fe cluster orchestrates conformational changes of the CO-dehydrogenase-acetyl-CoA synthase complex.
Authors: Jakob Ruickoldt / Julian Kreibich / Thomas Bick / Jae-Hun Jeoung / Benjamin R Duffus / Silke Leimkühler / Holger Dobbek / Petra Wendler /
Abstract: Catalytic metal clusters play critical roles in important enzymatic pathways such as carbon fixation and energy conservation. However, how ligand binding to the active-site metal regulates ...Catalytic metal clusters play critical roles in important enzymatic pathways such as carbon fixation and energy conservation. However, how ligand binding to the active-site metal regulates conformational changes critical for enzyme function is often not well understood. One carbon fixation pathway that relies heavily on metalloenzymes is the reductive acetyl-coenzyme A (acetyl-CoA) pathway. In this study, we investigated the catalysis of the last step of the reductive acetyl-CoA pathway by the CO-dehydrogenase (CODH)-acetyl-CoA synthase (ACS) complex from , focusing on how ligand binding to the nickel atom in the active site affects the conformational equilibrium of the enzyme. We captured six intermediate states of the enzyme by cryo-electron microscopy, with resolutions of 2.5-1.9 Å, and visualized reaction products bound to cluster A (an Ni,Ni-[4Fe4S] cluster) and identified several previously uncharacterized conformational states of CODH-ACS. The structures demonstrate how substrate binding controls conformational changes in the ACS subunit to prepare for the next catalytic step.
History
DepositionJun 26, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50754.png

Downloads & links

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Map

FileDownload / File: emd_50754.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap locally refined on the asymmetric unit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 368.128 Å		0.72 Å/pix.
x 512 pix.
= 368.128 Å		0.72 Å/pix.
x 512 pix.
= 368.128 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.719 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.32246295 - 0.69034284
Average (Standard dev.)-0.0001984835 (±0.011185099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 368.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50754_msk_1.map
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Half map: #2

Fileemd_50754_half_map_1.map
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Half map: #1

Fileemd_50754_half_map_2.map
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Sample components

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Entire : CODH/ACS complex

EntireName: CODH/ACS complex
Components
  • Complex: CODH/ACS complex
    • Protein or peptide: Carbon monoxide dehydrogenase
    • Protein or peptide: CO-methylating acetyl-CoA synthase
  • Ligand: Fe(3)-Ni(1)-S(4) cluster
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: NICKEL (II) ION
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: CODH/ACS complex

SupramoleculeName: CODH/ACS complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: half-closed state
Source (natural)Organism: Carboxydothermus hydrogenoformans (bacteria)

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Macromolecule #1: Carbon monoxide dehydrogenase

MacromoleculeName: Carbon monoxide dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: anaerobic carbon monoxide dehydrogenase
Source (natural)Organism: Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Molecular weightTheoretical: 73.172102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PRFRDLEHTS KPSKADRVWE PKNRKRTIDP AALEMLEKAE KDGVKTAFDR FVEMQPQCQF GYKGLCCRFC LQGPCRLPND DPSKKGICG ASAWTIAARS VGTLILTGAA AHNEHARHIA HALKELAEGK APDYKITDPD KLRRIAQRLG LDTQGKDDMT L AKEVAELA ...String:
PRFRDLEHTS KPSKADRVWE PKNRKRTIDP AALEMLEKAE KDGVKTAFDR FVEMQPQCQF GYKGLCCRFC LQGPCRLPND DPSKKGICG ASAWTIAARS VGTLILTGAA AHNEHARHIA HALKELAEGK APDYKITDPD KLRRIAQRLG LDTQGKDDMT L AKEVAELA LEDFARLPGF GENLWIKTTL NKERLEKYDE CNIMPSGIFG DISDLLAQAH IGNDDDPVNI TFSALRVALT DY AGMHIAT DFSDVLFGTP KPIVTEANLG VLDANKVNIA VHGHNPLLSE KVVDAAKELE EEAKAAGAEG INIVGMCCTG NEV LMRRGV HLATSFASSE LAIVTGAMDA VVVDVQCIMP GLKQVTECYH TRLITTSNIA KMPGTYHVPF HIENALESAK EIVR LGIEA FKQRVGKPVH IPEVKHKVVA GFSFEALMEI FAHVNQENPI RVLNDAILSG QLKGVVLFAG CNNLKRPQDE SHITI LKEM LKNDVFVVTT GCSAQAFAKH GFLRPEALEL AGEGLKSFIK MLEEKAGLQG QLPPAFFMGS CVDNTRASDI LVAMAK DLG VDTPKVPFVA SAPEAMSGKA VSIGTWFVTL GVPVHVGTMP PLEGSELFYS ITTQIASDVY GGYFMFEVDP VVAARKI LN ALEYRTWKLG VHKQTAEKFE TALCQNY

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Macromolecule #2: CO-methylating acetyl-CoA synthase

MacromoleculeName: CO-methylating acetyl-CoA synthase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: CO-methylating acetyl-CoA synthase
Source (natural)Organism: Carboxydothermus hydrogenoformans (bacteria)
Molecular weightTheoretical: 82.111172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: INFDQIFEGA IEPGKEPKRL FKEVYEGAIT ATSYAEILLS RAIEKYGPDH PVGYPDTAYF LPVIRAFSGE EVRTLKDMVP ILNRMRAQI KSELTFENAR LAGEATWYAA EIIEALRYLK HTPENPIVVP PWTGFIGDPV VRQYGIKMVD WTIPGEAIII G RAKDSKAA ...String:
INFDQIFEGA IEPGKEPKRL FKEVYEGAIT ATSYAEILLS RAIEKYGPDH PVGYPDTAYF LPVIRAFSGE EVRTLKDMVP ILNRMRAQI KSELTFENAR LAGEATWYAA EIIEALRYLK HTPENPIVVP PWTGFIGDPV VRQYGIKMVD WTIPGEAIII G RAKDSKAA KKIVDDLMGK GLMLFLCDEI IEQLLEENVK LGVDYIAYPL GNFTQVVHAA NYALRAGLMF GGIAPGLRDA HR DYQRRRV LAFVLYLGEH DMVKTAAAMG AIFTGFPVIT DQPLPEDKQI KDWFISEPDY DKIVQTALEV RGIKITSIDI DLP INFGPA FEGESIRKGD MHVEFGGGKT PSFELVRMVG PDEIEDGKVE VIGPDIDSVE PGGRLPIGIV VDIYGRKMQE DFEP VLERR IHYFTNYGEG FWHTAQRDLT WVRISKEAFA KGARLKHLGQ LLYAKFKQEF PSIVDRVQVT IYTDEQKVLE LREIA RKKY AERDARLREL SDEAVDTYYS CLLCQSFAPT HVCIVSPERV GLCGAISWLD AKAAYEINPN GPNQPIPKEG LIDPVK GQW ESFNEYIYKN SQRTIERMNL YTIMEYPMTS CGCFEAIMAY LPELNGFMIV NREHSGMTPI GMTFSTLAGM VGGGTQT PG FMGIGKSYIG SRKFVKADGG LARVVWMPKD LKEQLRSIIE ERAEEEGLGR DFIDKIADET VGTTVDEVLP FLEEKGHP A LSMEPLLRS

UniProtKB: CO-methylating acetyl-CoA synthase

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Macromolecule #3: Fe(3)-Ni(1)-S(4) cluster

MacromoleculeName: Fe(3)-Ni(1)-S(4) cluster / type: ligand / ID: 3 / Number of copies: 1 / Formula: RQM
Molecular weightTheoretical: 410.333 Da
Chemical component information

ChemComp-RQM:
Fe(3)-Ni(1)-S(4) cluster

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Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #5: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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Macromolecule #6: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 6 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 286 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.6
Component:
ConcentrationNameFormula
50.0 mMMops
150.0 mMsodium chlorideNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 291 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zkj

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146481
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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