9O6T | pdb_00009o6t

Structure of the human prohibitin complex in the open state

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-04-14 Released: 2025-05-07 
  • Deposition Author(s): Rose, K., Herrmann, E., Hurley, J.H.
  • Funding Organization(s): Aligning Science Across Parkinsons (ASAP), Alexander von Humboldt Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 22.0 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment.

Rose, K.Herrmann, E.Kakudji, E.Lizarrondo, J.Celebi, A.Y.Wilfling, F.Lewis, S.C.Hurley, J.H.

(2025) Proc Natl Acad Sci U S A 122: e2511890122-e2511890122

  • DOI: https://doi.org/10.1073/pnas.2511890122
  • Primary Citation of Related Structures:  
    9O6S, 9O6T

  • PubMed Abstract: 

    Defective mitochondrial quality control in response to loss of mitochondrial membrane polarization is implicated in Parkinson's disease by mutations in PINK1 and PRKN . Parkin-expressing U2 osteosarcoma (U2OS) cells were treated with the depolarizing agents oligomycin and antimycin A (OA) and subjected to cryo-focused ion beam milling and in situ cryo-electron tomography. Mitochondria were fragmented and devoid of matrix calcium phosphate crystals. Phagophores were visualized, with bridge-like lipid transporter densities connected to mitophagic phagophores. A subpopulation of ATP synthases relocalized from cristae to the inner boundary membrane. The structure of the dome-shaped prohibitin complex, a dodecamer of PHB1-PHB2 dimers, was determined in situ by subtomogram averaging in untreated and treated cells and found to exist in open and closed conformations, with the closed conformation being enriched by OA treatment. These findings provide a set of native snapshots of the manifold nano-structural consequences of mitochondrial depolarization and provide a baseline for future in situ dissection of Parkin-dependent mitophagy.


  • Organizational Affiliation
    • Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20815.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prohibitin-2
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
299Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99623 (Homo sapiens)
Explore Q99623 
Go to UniProtKB:  Q99623
PHAROS:  Q99623
GTEx:  ENSG00000215021 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99623
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Prohibitin 1
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
272Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P35232 (Homo sapiens)
Explore P35232 
Go to UniProtKB:  P35232
PHAROS:  P35232
GTEx:  ENSG00000167085 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35232
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 22.0 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Aligning Science Across Parkinsons (ASAP)United StatesASAP-000350
Alexander von Humboldt FoundationGermany--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM139168
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM139166

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references