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- EMDB-50904: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (C... -

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Basic information

Entry
Database: EMDB / ID: EMD-50904
TitleStructure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (focused refinement, class 3Ca)
Map data
Sample
  • Complex: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with corrinoid/iron-sulfur protein
Keywordsanaerobic CO2 fixation / acetyl-CoA synthesis / metalloenzyme / Wood-Ljungdahl pathway. / OXIDOREDUCTASE
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsYin MD / Lemaire ON / Wagner T / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Science / Year: 2025
Title: Conformational dynamics of a multienzyme complex in anaerobic carbon fixation.
Authors: Max Dongsheng Yin / Olivier N Lemaire / José Guadalupe Rosas Jiménez / Mélissa Belhamri / Anna Shevchenko / Gerhard Hummer / Tristan Wagner / Bonnie J Murphy /
Abstract: In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide ...In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). In this work, we present structural snapshots of the CODH/ACS from the gas-converting acetogen , characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site, and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer, and protect the reaction intermediates. Altogether, the structures allow us to draw a detailed reaction mechanism of this enzyme, which is crucial for CO fixation in anaerobic organisms.
History
DepositionJul 6, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50904.png

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Map

FileDownload / File: emd_50904.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 480 pix.
= 490.56 Å		1.02 Å/pix.
x 480 pix.
= 490.56 Å		1.02 Å/pix.
x 480 pix.
= 490.56 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.022 Å
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Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-1.0683184 - 1.9642708
Average (Standard dev.)-0.000057703834 (±0.036917705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 490.55997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50904_msk_1.map
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Half map: #1

Fileemd_50904_half_map_1.map
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Half map: #2

Fileemd_50904_half_map_2.map
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Sample components

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Entire : Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with...

EntireName: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with corrinoid/iron-sulfur protein
Components
  • Complex: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with corrinoid/iron-sulfur protein

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Supramolecule #1: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with...

SupramoleculeName: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with corrinoid/iron-sulfur protein
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Clostridium autoethanogenum DSM 10061 (bacteria)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72324
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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