9JVQ | pdb_00009jvq

Yeast Mitochondrial PORIN complex


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-025-62021-4
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-selective voltage-gated ion channel 1
A, B, C, D, E
A, B, C, D, E, F
283Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: POR1OMP2VDAC1YNL055CN2441YNL2441C
Membrane Entity: Yes 
UniProt
Find proteins for P04840 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04840 
Go to UniProtKB:  P04840
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04840
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

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