9JVQ | pdb_00009jvq

Yeast Mitochondrial PORIN complex

• PDB DOI: https://doi.org/10.2210/pdb9JVQ/pdb
• EM Map EMD-61843: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-10-09 Released: 2025-08-13 
• Deposition Author(s): Takeda, H., Endo, T., Kikkawa, M., Tsutsumi, A.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Oligomer-based functions of mitochondrial porin.

Takeda, H., Shinoda, S., Goto, C., Tsutsumi, A., Sakaue, H., Zhang, C., Hirashima, T., Konishi, Y., Ono, H., Yamamori, Y., Tomii, K., Shiino, H., Tamura, Y., Zuttion, S., Senger, B., Friant, S., Becker, H.D., Araiso, Y., Kobayashi, N., Kodera, N., Kikkawa, M., Endo, T.

(2025) Nat Commun 16: 6854-6854

• PubMed: 40715117 
• DOI: https://doi.org/10.1038/s41467-025-62021-4
• Primary Citation Related Structures: 
  9JVQ


• PubMed 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 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.

---

Organizational Affiliation: 
• Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.
Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.
Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
Faculty of Science, Yamagata University, Yamagata, Japan.
Université de Strasbourg, CNRS, Génétique Moléculaire, Génomique, Microbiologie, UMR7156, Strasbourg Cedex, France.
INSERM, Université de Strasbourg, UMRS1112, Laboratoire de Génétique Médicale, Centre de Recherche Biomédicale de Strasbourg (CRBS), Strasbourg, France.
Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan.
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa, Japan.
Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan. [e-mail].
Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 182.73 kDa 
• Atom Count: 12,827 
• Modeled Residue Count: 1,692 
• Deposited Residue Count: 1,698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-selective voltage-gated ion channel 1	A, B, C, D, E, F	283	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: POR1, OMP2, VDAC1, YNL055C, N2441, YNL2441C Membrane Entity: Yes
UniProt
Find proteins for P04840 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04840  Go to UniProtKB:  P04840

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Takeda, H., Endo, T., Kikkawa, M., Tsutsumi, A.

---

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release