[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleTOM20-driven E3 ligase recruitment regulates mitochondrial dynamics through PLD6.
Journal, issue, pagesNat Chem Biol, Vol. 22, Issue 1, Page 37-47, Year 2026
Publish dateApr 22, 2025
AuthorsAnat Raiff / Shidong Zhao / Aizat Bekturova / Colin Zenge / Shir Mazor / Xinyan Chen / Wenwen Ru / Yaara Makaros / Tslil Ast / Alban Ordureau / Chao Xu / Itay Koren /
PubMed AbstractMitochondrial homeostasis is maintained through complex regulatory mechanisms, including the balance of mitochondrial dynamics involving fusion and fission processes. A central player in this ...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.
External linksNat Chem Biol / PubMed:40263465 / PubMed Central
MethodsEM (single particle)
Resolution3.56 - 4.13 Å
Structure data

61196

9j77

EMDB-61196, PDB-9j77:
Cryo-EM structure of CRL2-FEM1B (dimer 1)
Method: EM (single particle) / Resolution: 3.56 Å

61197

9j78

EMDB-61197, PDB-9j78:
Cryo-EM structure of CRL2-FEM1B (dimer 2)
Method: EM (single particle) / Resolution: 3.88 Å

61198

9j79

EMDB-61198, PDB-9j79:
Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
Method: EM (single particle) / Resolution: 4.08 Å

61199

9j7a

EMDB-61199, PDB-9j7a:
local refinement of FEM1B bound with TOM20 (dimer)
Method: EM (single particle) / Resolution: 4.13 Å

61200

9j7b

EMDB-61200, PDB-9j7b:
local refinement of FEM1B bound with TOM20(tetramer)
Method: EM (single particle) / Resolution: 4.12 Å

61362

9jce

EMDB-61362, PDB-9jce:
local refinement of FEM1B bound with TOM20
Method: EM (single particle) / Resolution: 3.59 Å

63187

9lkx

EMDB-63187, PDB-9lkx:
local refinement of FEM1B bound with PLD6
Method: EM (single particle) / Resolution: 3.76 Å

63188

9lky

EMDB-63188, PDB-9lky:
Dimer of CRL2-FEM1B bound with PLD6
Method: EM (single particle) / Resolution: 3.93 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
KeywordsPROTEIN BINDING / ubiquitination E3 ligase / Cryo-EM

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more