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- EMDB-14433: Structure of the Escherichia coli formate hydrogenlyase complex (... -

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Basic information

Entry
Database: EMDB / ID: EMD-14433
TitleStructure of the Escherichia coli formate hydrogenlyase complex (aerobic preparation, focused refinement peripheral arm)
Map data
Sample
  • Complex: Escherichia coli formate hydrogenlyase complex
KeywordsFHL / group-4 membrane bound hydrogenase / [NiFe] hydrogenase / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSteinhilper R / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli.
Authors: Ralf Steinhilper / Gabriele Höff / Johann Heider / Bonnie J Murphy /
Abstract: The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase ...The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H during fermentation, its reversibility, allowing H-dependent CO reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex.
History
DepositionFeb 23, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14433.png

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Map

FileDownload / File: emd_14433.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.)
0.83 Å/pix.
x 480 pix.
= 397.44 Å		0.83 Å/pix.
x 480 pix.
= 397.44 Å		0.83 Å/pix.
x 480 pix.
= 397.44 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
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Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05736603 - 0.12958622
Average (Standard dev.)0.000015614807 (±0.0019403126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 397.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14433_msk_1.map
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Half map: #1

Fileemd_14433_half_map_1.map
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Half map: #2

Fileemd_14433_half_map_2.map
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Sample components

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Entire : Escherichia coli formate hydrogenlyase complex

EntireName: Escherichia coli formate hydrogenlyase complex
Components
  • Complex: Escherichia coli formate hydrogenlyase complex

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Supramolecule #1: Escherichia coli formate hydrogenlyase complex

SupramoleculeName: Escherichia coli formate hydrogenlyase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 72.0 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: 2.2 µm / Nominal defocus min: 1.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 90459
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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