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- EMDB-50729: Extended state of carbonylated CODH/ACS (3D flex consensus map) -

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Basic information

Entry
Database: EMDB / ID: EMD-50729
TitleExtended state of carbonylated CODH/ACS (3D flex consensus map)
Map data
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
DepositionJun 21, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50729.png

Downloads & links

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Map

FileDownload / File: emd_50729.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 360 pix.
= 368.136 Å		1.02 Å/pix.
x 360 pix.
= 368.136 Å		1.02 Å/pix.
x 360 pix.
= 368.136 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0226 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00235
Minimum - Maximum-0.022260945 - 0.049181744
Average (Standard dev.)0.000022436656 (±0.00064882834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 368.13602 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D flex canonical map

Fileemd_50729_additional_1.map
Annotation3D flex canonical map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D-flex half map

Fileemd_50729_half_map_1.map
Annotation3D-flex half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D-flex half map

Fileemd_50729_half_map_2.map
Annotation3D-flex 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: 3D flexible refinement
Details: Resolution is not defined as this is a Consensus volume from 3D Flex
Number images used: 39000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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