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- EMDB-52973: focused map of the junction between peripheral arm and membrane a... -

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Basic information

Entry
Database: EMDB / ID: EMD-52973
Titlefocused map of the junction between peripheral arm and membrane arm of E. coli respiratory complex I variant V96P/N142M (NuoE)
Map dataFocused map of the junction of complex I between peripheral arm and membrane arm for building the composite map.
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: To Be Published
Title: Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I
Authors: Wohlwend D / Seifermann T / Gnandt E / Vranas M / Gerhardt S / Friedrich T
History
DepositionFeb 27, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52973.png

Downloads & links

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Map

FileDownload / File: emd_52973.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of the junction of complex I between peripheral arm and membrane arm for building the composite map.
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: 0.2
Minimum - Maximum-0.5267461 - 1.2507856
Average (Standard dev.)-0.00073996687 (±0.02050914)
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 A of focused map of the junction of complex I

Fileemd_52973_half_map_1.map
AnnotationHalf map A of focused map of the junction of complex I
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of focused map of the junction of complex I

Fileemd_52973_half_map_2.map
AnnotationHalf map B of focused map of the junction of complex I
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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