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- EMDB-55061: VDAC1 in cMSP1D1 nanodiscs, monomeric. -

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Basic information

Entry
Database: EMDB / ID: EMD-55061
TitleVDAC1 in cMSP1D1 nanodiscs, monomeric.
Map dataSharpened map.
Sample
  • Complex: Human VDAC1 in cMSP1D1 circularized nanodiscs. Monomeric form.
KeywordsVDAC1 / cMSP / nanodisc / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.21 Å
AuthorsBroutzakis G / Gatsogiannis C
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)201302640 Germany
German Research Foundation (DFG)496113311 Germany
German Research Foundation (DFG)424228829 Germany
German Research Foundation (DFG)386797833 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of apoptosis induction by the mitochondrial voltage-dependent anion channel.
Authors: Melina Daniilidis / Umut Günsel / Georgios Broutzakis / Kira D Leitl / Robert Janowski / Kai Fredriksson / Dierk Niessing / Christos Gatsogiannis / Franz Hagn /
Abstract: The voltage-dependent anion channel (VDAC) is the main gateway for metabolites across the mitochondrial outer membrane. VDAC oligomers are connected to apoptosis induced by various stimuli. However, ...The voltage-dependent anion channel (VDAC) is the main gateway for metabolites across the mitochondrial outer membrane. VDAC oligomers are connected to apoptosis induced by various stimuli. However, the mechanistic and structural basis of apoptosis induction by VDAC remains poorly understood. Here, using cryo-EM and NMR we show that VDAC1 oligomerization or confinement in small lipid nanodiscs triggers the exposure of its N-terminal α-helix (VDAC1-N) which becomes available for partner protein binding. NMR and X-ray crystallography data show that VDAC1-N forms a complex with the BH3 binding groove of the anti-apoptotic Bcl2 protein BclxL. Biochemical assays demonstrate that VDAC1-N exhibits a pro-apoptotic function by promoting pore formation of the executor Bcl2 protein Bak via neutralization of BclxL. This mechanism is reminiscent of BH3-only sensitizer Bcl2 proteins that are efficient inducers of Bax/Bak-mediated mitochondrial outer membrane permeabilization and ultimately apoptosis. The VDAC pathway most likely responds to mitochondrial stress or damage.
History
DepositionSep 15, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55061.png

Downloads & links

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Map

FileDownload / File: emd_55061.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 168 pix.
= 220.802 Å		1.31 Å/pix.
x 168 pix.
= 220.802 Å		1.31 Å/pix.
x 168 pix.
= 220.802 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3143 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.44571498 - 0.6369042
Average (Standard dev.)-0.000050746203 (±0.0226831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 220.80238 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55061_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_55061_msk_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half-map B.

Fileemd_55061_half_map_1.map
AnnotationHalf-map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B.

Fileemd_55061_half_map_2.map
AnnotationHalf-map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human VDAC1 in cMSP1D1 circularized nanodiscs. Monomeric form.

EntireName: Human VDAC1 in cMSP1D1 circularized nanodiscs. Monomeric form.
Components
  • Complex: Human VDAC1 in cMSP1D1 circularized nanodiscs. Monomeric form.

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Supramolecule #1: Human VDAC1 in cMSP1D1 circularized nanodiscs. Monomeric form.

SupramoleculeName: Human VDAC1 in cMSP1D1 circularized nanodiscs. Monomeric form.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration2.5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClSodium Chloride
0.5 mMC10H16N2O8EDTA
2.0 mMC4H10O2S2DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286.15 K / Instrument: FEI VITROBOT MARK IV / Details: UltrAuFoil R 1.2/1.3, 300 mesh.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 270000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 169625
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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