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- EMDB-52971: focused map of the peripheral arm of E. coli complex I variant V9... -

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Basic information

Entry
Database: EMDB / ID: EMD-52971
Titlefocused map of the peripheral arm of E. coli complex I variant V96P/N142M (NuoE)
Map dataFocused map of the peripheral arm used to generate the composite map of the entire complex I
Sample
  • Complex: Respiratory complex I
KeywordsRespiratory chain / Complex I / NADH ubiquinone oxidoreductase / electron transport / proton transport / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsSeifermann T / Wohlwend D / Friedrich T
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1140/11-2 Germany
German Research Foundation (DFG)278002225 Germany
CitationJournal: Structure / Year: 2025
Title: Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I.
Authors: Daniel Wohlwend / Thilo Seifermann / Emmanuel Gnandt / Marta Vranas / Stefan Gerhardt / Thorsten Friedrich /
Abstract: Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. ...Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.
History
DepositionFeb 27, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52971.png

Downloads & links

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Map

FileDownload / File: emd_52971.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of the peripheral arm used to generate the composite map of the entire complex I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 400 pix.
= 457.6 Å		1.14 Å/pix.
x 400 pix.
= 457.6 Å		1.14 Å/pix.
x 400 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.50633454 - 1.3170265
Average (Standard dev.)-0.00070804224 (±0.023262223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 457.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B of focused map of the peripheral arm

Fileemd_52971_half_map_1.map
AnnotationHalf Map B of focused map of the peripheral arm
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A of focused map of the peripheral arm

Fileemd_52971_half_map_2.map
AnnotationHalf Map A of focused map of the peripheral arm
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Respiratory complex I

EntireName: Respiratory complex I
Components
  • Complex: Respiratory complex I

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Supramolecule #1: Respiratory complex I

SupramoleculeName: Respiratory complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 542 KDa

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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

Concentration10 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
50.0 mMNaClsodium chloride
50.0 mMC6H13NO4SMES
5.0 mMMgCl2magnesium chloride
10.0 %C3H8O3glycerol
0.005 %C47H88O22lauryl maltose neopentyl glycol

Details: 50 mM MES/NaOH, pH 6.0, 50 mM NaCl, 5 mM MgCl2, 10 % (v/v) glycerol, 0.005 % (w/v) LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time for 6 s with filter paper.
DetailsFos-choline-10 (0.2% (v/v) final concentration) was added before blotting. blotted for 6 s with filter paper and flash frozen in liquid ethane cooled by liquid nitrogen using a Vitrobot Mark IV (Thermo Fisher Scientific) at 90% humidity and 277 K.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7z7s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 95103
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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