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- EMDB-15053: In situ structure of HDCR filaments -

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Basic information

Entry
Database: EMDB / ID: EMD-15053
TitleIn situ structure of HDCR filaments
Map data
Sample
  • Complex: Hydrogen-dependent CO2 reductase
Biological speciesThermoanaerobacter kivui (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 17.0 Å
AuthorsDietrich HM / Righetto RD / Kumar A / Wietrzynski W / Schuller SK / Trischler R / Wagner J / Schwarz FM / Engel BD / Mueller V / Schuller JM
Funding support Germany, European Union, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3364/1-1 Germany
European Research Council (ERC)741791European Union
German Research Foundation (DFG)FOR 2092 Germany
Alexander von Humboldt Foundation Germany
German Research Foundation (DFG)20016/446 Germany
CitationJournal: Nature / Year: 2022
Title: Membrane-anchored HDCR nanowires drive hydrogen-powered CO fixation.
Authors: Helge M Dietrich / Ricardo D Righetto / Anuj Kumar / Wojciech Wietrzynski / Raphael Trischler / Sandra K Schuller / Jonathan Wagner / Fabian M Schwarz / Benjamin D Engel / Volker Müller / Jan M Schuller /
Abstract: Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO ...Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO fixation-hydrogen-dependent CO reductase (HDCR)-which directly converts H and CO into formic acid. HDCR reduces CO with a higher activity than any other known biological or chemical catalyst, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.
History
DepositionMay 29, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15053.png

Downloads & links

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Map

FileDownload / File: emd_15053.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
7.04 Å/pix.
x 96 pix.
= 675.84 Å		7.04 Å/pix.
x 96 pix.
= 675.84 Å		7.04 Å/pix.
x 96 pix.
= 675.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 7.04 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.80754805 - 1.6837109
Average (Standard dev.)-1.2043012e-11 (±0.13566563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 675.83997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15053_msk_1.map
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Half map: #1

Fileemd_15053_half_map_1.map
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Half map: #2

Fileemd_15053_half_map_2.map
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Sample components

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Entire : Hydrogen-dependent CO2 reductase

EntireName: Hydrogen-dependent CO2 reductase
Components
  • Complex: Hydrogen-dependent CO2 reductase

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Supramolecule #1: Hydrogen-dependent CO2 reductase

SupramoleculeName: Hydrogen-dependent CO2 reductase / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.5 µm / Nominal magnification: 42000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsDose-symmetric tilt-series were acquired (Hagen et al., 2017), starting at +10 degrees to match the pre-tilt of the lamella (i.e. from -50 to +70 degrees).
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 19 / Number images used: 12545 / Software - Name: STOPGAP (ver. 0.7)
CTF correctionSoftware: (Name: CTFFIND (ver. 4), NOVACTF)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: STOPGAP (ver. 0.7)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP (ver. 0.7) / Number subtomograms used: 6727
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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