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- PDB-9jvq: Yeast Mitochondrial PORIN complex -

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Basic information

Entry
Database: PDB / ID: 9jvq
TitleYeast Mitochondrial PORIN complex
ComponentsNon-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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTakeda, H. / Endo, T. / Kikkawa, M. / Tsutsumi, A.
Funding support Japan, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-selective voltage-gated ion channel 1
B: Non-selective voltage-gated ion channel 1
C: Non-selective voltage-gated ion channel 1
D: Non-selective voltage-gated ion channel 1
E: Non-selective voltage-gated ion channel 1
F: Non-selective voltage-gated ion channel 1


Theoretical massNumber of molelcules
Total (without water)182,7326
Polymers182,7326
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Non-selective voltage-gated ion channel 1 / Outer mitochondrial membrane protein porin 1 / Voltage-dependent anion-selective channel protein 1 / VDAC-1


Mass: 30455.377 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: POR1, OMP2, VDAC1, YNL055C, N2441, YNL2441C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04840
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast mitochondrial PORIN complex (VDAC1 hexamer) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78760 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313091
ELECTRON MICROSCOPYf_angle_d0.73817800
ELECTRON MICROSCOPYf_dihedral_angle_d4.2331784
ELECTRON MICROSCOPYf_chiral_restr0.0462070
ELECTRON MICROSCOPYf_plane_restr0.0042303

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