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- EMDB-50837: CODH/ACS in the loose extended state in the presence of CoA (3D f... -

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Basic information

Entry
Database: EMDB / ID: EMD-50837
TitleCODH/ACS in the loose extended state in the presence of CoA (3D flex consensus map)
Map data3D flex consensus map
Sample
  • Complex: CODH/ACS complex
    • Protein or peptide: CO-dehydrogenase
    • Protein or peptide: Acetyl-CoA synthase
KeywordsCODH / ACS / CO2 fixation / reductive acetyl-CoA pathway / Wood-Ljungdahl pathway / OXIDOREDUCTASE
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 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
DepositionJul 1, 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_50837.png

Downloads & links

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Map

FileDownload / File: emd_50837.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D flex consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.88 Å/pix.
x 128 pix.
= 368.128 Å		2.88 Å/pix.
x 128 pix.
= 368.128 Å		2.88 Å/pix.
x 128 pix.
= 368.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.876 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0179
Minimum - Maximum-0.007488361 - 0.34960157
Average (Standard dev.)0.00032377365 (±0.0045004818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 368.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D flex reconstructed map

Fileemd_50837_additional_1.map
Annotation3D flex reconstructed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D flex reconstructed half-map

Fileemd_50837_half_map_1.map
Annotation3D flex reconstructed half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D flex reconstructed half-map

Fileemd_50837_half_map_2.map
Annotation3D flex reconstructed half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: CO-dehydrogenase
    • Protein or peptide: Acetyl-CoA synthase

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Supramolecule #1: CODH/ACS complex

SupramoleculeName: CODH/ACS complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: extended state
Source (natural)Organism: Carboxydothermus hydrogenoformans (bacteria)

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Macromolecule #1: CO-dehydrogenase

MacromoleculeName: CO-dehydrogenase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Carboxydothermus hydrogenoformans (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PRFRDLEHTS KPSKADRVWE PKNRKRTIDP AALEMLEKAE KDGVKTAFDR FVEMQPQCQF GYKGLCCRF CLQGPCRLPN DDPSKKGICG ASAWTIAARS VGTLILTGAA AHNEHARHIA H ALKELAEG KAPDYKITDP DKLRRIAQRL GLDTQGKDDM TLAKEVAELA ...String:
PRFRDLEHTS KPSKADRVWE PKNRKRTIDP AALEMLEKAE KDGVKTAFDR FVEMQPQCQF GYKGLCCRF CLQGPCRLPN DDPSKKGICG ASAWTIAARS VGTLILTGAA AHNEHARHIA H ALKELAEG KAPDYKITDP DKLRRIAQRL GLDTQGKDDM TLAKEVAELA LEDFARLPGF GE NLWIKTT LNKERLEKYD ECNIMPSGIF GDISDLLAQA HIGNDDDPVN ITFSALRVAL TDY AGMHIA TDFSDVLFGT PKPIVTEANL GVLDANKVNI AVHGHNPLLS EKVVDAAKEL EEEA KAAGA EGINIVGMCC TGNEVLMRRG VHLATSFASS ELAIVTGAMD AVVVDVQCIM PGLKQ VTEC YHTRLITTSN IAKMPGTYHV PFHIENALES AKEIVRLGIE AFKQRVGKPV HIPEVK HKV VAGFSFEALM EIFAHVNQEN PIRVLNDAIL SGQLKGVVLF AGCNNLKRPQ DESHITI LK EMLKNDVFVV TTGCSAQAFA KHGFLRPEAL ELAGEGLKSF IKMLEEKAGL QGQLPPAF F MGSCVDNTRA SDILVAMAKD LGVDTPKVPF VASAPEAMSG KAVSIGTWFV TLGVPVHVG TMPPLEGSEL FYSITTQIAS DVYGGYFMFE VDPVVAARKI LNALEYRTWK LGVHKQTAEK FETALCQNY

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Macromolecule #2: Acetyl-CoA synthase

MacromoleculeName: Acetyl-CoA synthase / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Carboxydothermus hydrogenoformans (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: INFDQIFEGA IEPGKEPKRL FKEVYEGAIT ATSYAEILLS RAIEKYGPDH PVGYPDTAYF LPVIRAFSG EEVRTLKDMV PILNRMRAQI KSELTFENAR LAGEATWYAA EIIEALRYLK H TPENPIVV PPWTGFIGDP VVRQYGIKMV DWTIPGEAII IGRAKDSKAA ...String:
INFDQIFEGA IEPGKEPKRL FKEVYEGAIT ATSYAEILLS RAIEKYGPDH PVGYPDTAYF LPVIRAFSG EEVRTLKDMV PILNRMRAQI KSELTFENAR LAGEATWYAA EIIEALRYLK H TPENPIVV PPWTGFIGDP VVRQYGIKMV DWTIPGEAII IGRAKDSKAA KKIVDDLMGK GL MLFLCDE IIEQLLEENV KLGVDYIAYP LGNFTQVVHA ANYALRAGLM FGGIAPGLRD AHR DYQRRR VLAFVLYLGE HDMVKTAAAM GAIFTGFPVI TDQPLPEDKQ IKDWFISEPD YDKI VQTAL EVRGIKITSI DIDLPINFGP AFEGESIRKG DMHVEFGGGK TPSFELVRMV GPDEI EDGK VEVIGPDIDS VEPGGRLPIG IVVDIYGRKM QEDFEPVLER RIHYFTNYGE GFWHTA QRD LTWVRISKEA FAKGARLKHL GQLLYAKFKQ EFPSIVDRVQ VTIYTDEQKV LELREIA RK KYAERDARLR ELSDEAVDTY YSCLLCQSFA PTHVCIVSPE RVGLCGAISW LDAKAAYE I NPNGPNQPIP KEGLIDPVKG QWESFNEYIY KNSQRTIERM NLYTIMEYPM TSCGCFEAI MAYLPELNGF MIVNREHSGM TPIGMTFSTL AGMVGGGTQT PGFMGIGKSY IGSRKFVKAD GGLARVVWM PKDLKEQLRS IIEERAEEEG LGRDFIDKIA DETVGTTVDE VLPFLEEKGH P ALSMEPLL RS

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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: 51.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 4.3.0)
Software - details: 3Dflex was used to reconstruct the density
Details: resolution is not determinable. This is a consensus map from 3DFlex
Number images used: 161469
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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