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- EMDB-61843: Yeast Mitochondrial PORIN complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61843
TitleYeast Mitochondrial PORIN complex
Map data
Sample
  • Complex: Yeast mitochondrial PORIN complex (VDAC1 hexamer)
    • Protein or peptide: Non-selective voltage-gated ion channel 1
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


mitochondrial inner-outer membrane contact site / DNA transport / Pyruvate metabolism / PINK1-PRKN Mediated Mitophagy / voltage-gated monoatomic anion channel activity / phospholipid scramblase activity / phospholipid translocation / porin activity / pore complex / ubiquinone binding ...mitochondrial inner-outer membrane contact site / DNA transport / Pyruvate metabolism / PINK1-PRKN Mediated Mitophagy / voltage-gated monoatomic anion channel activity / phospholipid scramblase activity / phospholipid translocation / porin activity / pore complex / ubiquinone binding / monoatomic ion transport / cell redox homeostasis / mitochondrion organization / mitochondrial intermembrane space / positive regulation of protein import into nucleus / mitochondrial outer membrane / apoptotic process / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
Non-selective voltage-gated ion channel 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTakeda H / Endo T / Kikkawa M / Tsutsumi A
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Commun / Year: 2025
Title: Oligomer-based functions of mitochondrial porin.
Authors: Hironori Takeda / Saori Shinoda / Chiho Goto / Akihisa Tsutsumi / Haruka Sakaue / Chunming Zhang / Takashi Hirashima / Yuta Konishi / Haruka Ono / Yu Yamamori / Kentaro Tomii / Hiroya Shiino ...Authors: Hironori Takeda / Saori Shinoda / Chiho Goto / Akihisa Tsutsumi / Haruka Sakaue / Chunming Zhang / Takashi Hirashima / Yuta Konishi / Haruka Ono / Yu Yamamori / Kentaro Tomii / Hiroya Shiino / Yasushi Tamura / Solène Zuttion / Bruno Senger / Sylvie Friant / Hubert D Becker / Yuhei Araiso / Nanako Kobayashi / Noriyuki Kodera / Masahide Kikkawa / Toshiya Endo /
Abstract: Porin, or the voltage-dependent anion channel (VDAC), is a primary β-barrel channel in the mitochondrial outer membrane. It transports small metabolites and ions through its β-barrel pore and plays ...Porin, or the voltage-dependent anion channel (VDAC), is a primary β-barrel channel in the mitochondrial outer membrane. It transports small metabolites and ions through its β-barrel pore and plays key roles in apoptosis and inflammatory response. Here we report the cryo-electron microscopy structure of yeast porin (Por1) in its hexameric form at 3.2 Å resolution. This structure allows us to introduce various mutations at the protomer interfaces, uncovering three critical functions of Por1 assembly beyond transport. Por1 binds unassembled Tom22, a subunit of the mitochondrial protein import gate (the TOM complex), to facilitate protein import into the intermembrane space, maintains proper mitochondrial lipid composition in the outer membrane through lipid scramblase activity, and contributes to the retention and regulated loss of mitochondrial DNA, in cooperation with nucleases identified through screening enabled by the obtained Por1 mutant.
History
DepositionOct 9, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61843.png

Downloads & links

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Map

FileDownload / File: emd_61843.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 256 pix.
= 318.72 Å		1.25 Å/pix.
x 256 pix.
= 318.72 Å		1.25 Å/pix.
x 256 pix.
= 318.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00018
Minimum - Maximum-0.0027521143 - 0.0033103367
Average (Standard dev.)0.00000018461769 (±0.00005898587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61843_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61843_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Yeast mitochondrial PORIN complex (VDAC1 hexamer)

EntireName: Yeast mitochondrial PORIN complex (VDAC1 hexamer)
Components
  • Complex: Yeast mitochondrial PORIN complex (VDAC1 hexamer)
    • Protein or peptide: Non-selective voltage-gated ion channel 1

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Supramolecule #1: Yeast mitochondrial PORIN complex (VDAC1 hexamer)

SupramoleculeName: Yeast mitochondrial PORIN complex (VDAC1 hexamer) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Non-selective voltage-gated ion channel 1

MacromoleculeName: Non-selective voltage-gated ion channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 30.455377 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSPPVYSDIS RNINDLLNKD FYHATPAAFD VQTTTANGIK FSLKAKQPVK DGPLSTNVEA KLNDKQTGLG LTQGWSNTNN LQTKLEFAN LTPGLKNELI TSLTPGVAKS AVLNTTFTQP FFTARGAFDL CLKSPTFVGD LTMAHEGIVG GAEFGYDISA G SISRYAMA ...String:
MSPPVYSDIS RNINDLLNKD FYHATPAAFD VQTTTANGIK FSLKAKQPVK DGPLSTNVEA KLNDKQTGLG LTQGWSNTNN LQTKLEFAN LTPGLKNELI TSLTPGVAKS AVLNTTFTQP FFTARGAFDL CLKSPTFVGD LTMAHEGIVG GAEFGYDISA G SISRYAMA LSYFAKDYSL GATLNNEQIT TVDFFQNVNA FLQVGAKATM NCKLPNSNVN IEFATRYLPD ASSQVKAKVS DS GIVTLAY KQLLRPGVTL GVGSSFDALK LSEPVHKLGW SLSFDA

UniProtKB: Non-selective voltage-gated ion channel 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 78760
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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