9JCE | pdb_00009jce

local refinement of FEM1B bound with TOM20


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9JCE

This is version 1.4 of the entry. See complete history

Literature

TOM20-driven E3 ligase recruitment regulates mitochondrial dynamics through PLD6.

Raiff, A.Zhao, S.Bekturova, A.Zenge, C.Mazor, S.Chen, X.Ru, W.Makaros, Y.Ast, T.Ordureau, A.Xu, C.Koren, I.

(2026) Nat Chem Biol 22: 37-47

  • DOI: https://doi.org/10.1038/s41589-025-01894-4
  • Primary Citation Related Structures: 
    9J77, 9J78, 9J79, 9J7A, 9J7B, 9JCE, 9LKX, 9LKY

  • PubMed Abstract: 

    Mitochondrial homeostasis is maintained through complex regulatory mechanisms, including the balance of mitochondrial dynamics involving fusion and fission processes. A central player in this regulation is the ubiquitin-proteasome system (UPS), which controls the degradation of pivotal mitochondrial proteins. In this study, we identified cullin-RING E3 ligase 2 (CRL2) and its substrate receptor, FEM1B, as critical regulators of mitochondrial dynamics. Through proteomic analysis, we demonstrate here that FEM1B controls the turnover of PLD6, a key regulator of mitochondrial dynamics. Using structural and biochemical approaches, we show that FEM1B physically interacts with PLD6 and that this interaction is facilitated by the direct association of FEM1B with the mitochondrial import receptor TOM20. Ablation of FEM1B or disruption of the FEM1B-TOM20 interaction impairs PLD6 degradation and induces mitochondrial defects, phenocopying PLD6 overexpression. These findings underscore the importance of FEM1B in maintaining mitochondrial morphology and provide further mechanistic insights into how the UPS regulates mitochondrial homeostasis.


  • Organizational Affiliation
    • Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.

Macromolecule Content 

  • Total Structure Weight: 84.98 kDa 
  • Atom Count: 5,511 
  • Modeled Residue Count: 704 
  • Deposited Residue Count: 757 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein fem-1 homolog B627Homo sapiensMutation(s): 0 
Gene Names: FEM1BF1AAKIAA0396
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK73 (Homo sapiens)
Explore Q9UK73 
Go to UniProtKB:  Q9UK73
PHAROS:  Q9UK73
GTEx:  ENSG00000169018 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UK73
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly-UNKB [auth C]9Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM20 homologC [auth B]121Homo sapiensMutation(s): 0 
Gene Names: TOMM20KIAA0016
UniProt & NIH Common Fund Data Resources
Find proteins for Q15388 (Homo sapiens)
Explore Q15388 
Go to UniProtKB:  Q15388
PHAROS:  Q15388
GTEx:  ENSG00000173726 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15388
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-07
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-23
    Changes: Data collection
  • Version 1.4: 2026-01-07
    Changes: Data collection, Database references