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- EMDB-56604: CryoEM structure of carbon monoxide dehydrogenase from Ruminococc... -

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Basic information

Entry
Database: EMDB / ID: EMD-56604
TitleCryoEM structure of carbon monoxide dehydrogenase from Ruminococcus flavefaciens
Map dataCryoSPARC non-uniform refinement map of RfCODH
Sample
  • Complex: Homodimer of carbon-monoxide dehydrogenase from Ruminococcus flavefaciens
    • Protein or peptide: anaerobic carbon-monoxide dehydrogenase
  • Ligand: IRON/SULFUR CLUSTER
Keywordscarbon monoxide dehydrogenase / CODH / metalloenzyme / iron sulfur protein / anaerobic enzyme / OXIDOREDUCTASE
Biological speciesRuminococcus flavefaciens ATCC 19208 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsSrinivas V / Hogbom M
Funding support Sweden, Denmark, 3 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2023.0201 Sweden
Swedish Research Council2017-04018 Sweden
Novo Nordisk FoundationNNF21OC0066716 Denmark
CitationJournal: Angew Chem Int Ed Engl / Year: 2026
Title: Beyond Canonical CO Oxidation: Structural and Evolutionary Insights Into a Non-Canonical Carbon Monoxide Dehydrogenase.
Authors: Maximilian Böhm / Vivek Srinivas / Benjamin Wiseman / Ping Huang / Moritz Senger / Martin Högbom / Henrik Land /
Abstract: Carbon monoxide dehydrogenases (CODHs) catalyse the reversible oxidation of CO to CO and play central roles in microbial carbon metabolism. While well-characterised CODHs from different phylogenetic ...Carbon monoxide dehydrogenases (CODHs) catalyse the reversible oxidation of CO to CO and play central roles in microbial carbon metabolism. While well-characterised CODHs from different phylogenetic backgrounds exhibit high bidirectional activity, the enigmatic clade B remains functionally uncharacterised. Here, we present the first structural and biochemical characterisation of a clade B CODH from Ruminococcus flavefaciens (RfCODH). It reveals striking divergence from canonical enzymes. A new anaerobic cryo-EM workflow was developed, carried out entirely under anoxic conditions by manual blotting and plunge freezing. It resulted in a 2.53 Å RfCODH structure. The structure adopts the typical CODH fold, but exhibits blocked gas channels, a compromised proton transfer pathway and disrupted cofactor coordination. This provides a structural rationale for RfCODH's severely attenuated CO oxidation activity (13 mU/mg vs. 900 U/mg for the well-studied ChCODH-II). EPR spectroscopy reveals unique oxidised C-cluster states not previously characterised in CODHs. Mirror tree analysis hints to co-evolution between clade B CODHs and associated ABC transporter substrate-binding proteins, suggesting these enzymes function in metabolism of substrates imported via the ABC transporter module. All findings indicate evolutionary repurposing of the CODH scaffold for alternative physiological functions.
History
DepositionFeb 6, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56604.png

Downloads & links

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Map

FileDownload / File: emd_56604.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC non-uniform refinement map of RfCODH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 320 pix.
= 208. Å		0.65 Å/pix.
x 320 pix.
= 208. Å		0.65 Å/pix.
x 320 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.1768189 - 0.52693623
Average (Standard dev.)-0.00023099515 (±0.012953721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56604_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoSPARC non-uniform refinement half-map B of RfCODH

Fileemd_56604_half_map_1.map
AnnotationCryoSPARC non-uniform refinement half-map B of RfCODH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoSPARC non-uniform refinement half-map A of RfCODH

Fileemd_56604_half_map_2.map
AnnotationCryoSPARC non-uniform refinement half-map A of RfCODH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimer of carbon-monoxide dehydrogenase from Ruminococcus flav...

EntireName: Homodimer of carbon-monoxide dehydrogenase from Ruminococcus flavefaciens
Components
  • Complex: Homodimer of carbon-monoxide dehydrogenase from Ruminococcus flavefaciens
    • Protein or peptide: anaerobic carbon-monoxide dehydrogenase
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: Homodimer of carbon-monoxide dehydrogenase from Ruminococcus flav...

SupramoleculeName: Homodimer of carbon-monoxide dehydrogenase from Ruminococcus flavefaciens
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ruminococcus flavefaciens ATCC 19208 (bacteria)
Molecular weightTheoretical: 158 KDa

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Macromolecule #1: anaerobic carbon-monoxide dehydrogenase

MacromoleculeName: anaerobic carbon-monoxide dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: anaerobic carbon monoxide dehydrogenase
Source (natural)Organism: Ruminococcus flavefaciens ATCC 19208 (bacteria)
Molecular weightTheoretical: 78.97725 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKKDHDHCH DHEHKHDHDH AHHEHSPAHI HSHRNIIGFD EHGIPTVILK ASHGEGEQDD PQAFIKDYMN AVSEYRKTFP TKQDVIEQT PDPAVREMLL RMEQLGIDTA FDRFDQQKPQ CNFGLAGVCC KICNMGPCRV TAKSPKGVCG ADADLIVARN L LRSAAAGA ...String:
MSKKDHDHCH DHEHKHDHDH AHHEHSPAHI HSHRNIIGFD EHGIPTVILK ASHGEGEQDD PQAFIKDYMN AVSEYRKTFP TKQDVIEQT PDPAVREMLL RMEQLGIDTA FDRFDQQKPQ CNFGLAGVCC KICNMGPCRV TAKSPKGVCG ADADLIVARN L LRSAAAGA AQHGMHAREV MLALKWAAEG KLDVPILGEQ KIRATAEAFG IKQKNRQLKN VAKDLADALL EDLSRTVPDE YK TISACAV PERQQVWKDL DILPISAYHE VFEAYHKSGC ATDGDWKSVM QQFLRCGLAF TFSGVVGASI ATDSLFGVGD RVT SKVNIG ALEKGYVNIA VHGHLPLLVS QIVEAGKRED LIELAKSKGA KGIRFYGICC SGLSAMYRYA GVIPLSNAVS AELI LGTGA LDLWVADVQD VFPSIMEVAH CFKTTVVTTS ESARLPGAER YEYDHHHSNI DETKALAEKI VRRAIESFEA RKGIP VYIP PYEVEAEVGF SVEYIHKRFG SMKPLAEAIK DGRILGIVNM VGCNNPKVLY EKCIVDVADV LLKNNVLIIS NGCASF PLM KLGYCAVSGK EKAGDSLREF LEPDLPPVWH VGECIDNTRS SGIFAGVAGA LGHKMYEMPF AFSSPEWGNE KGIDAAL GF RLNGISSYHC VEAQIYGSKN VIEFLKYGTL ETLGSSMNVD TDPVKLGEKI VADMKAKRKA LGWDKSSGWS HPQFEK

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Macromolecule #2: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 2 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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: 8 / Details: 50 mM Tris-HCl pH 8, 20 mM NaCl, 5 % w/v glycerol,
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 0 %
Details: Vetrification carried out by manually plunge-freezing in a nitrogen glove box.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.65 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: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. V4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.7.1) / Number images used: 123492
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-28lw:
CryoEM structure of carbon monoxide dehydrogenase from Ruminococcus flavefaciens

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