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- PDB-9jce: local refinement of FEM1B bound with TOM20 -

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Basic information

Entry
Database: PDB / ID: 9jce
Titlelocal refinement of FEM1B bound with TOM20
Components
  • Mitochondrial import receptor subunit TOM20 homolog
  • Poly-UNK
  • Protein fem-1 homolog B
KeywordsPROTEIN BINDING / ubiquitination E3 ligase / Cryo-EM
Function / homology
Function and homology information


tRNA import into mitochondrion / TOM complex / regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein-transporting ATPase activity ...tRNA import into mitochondrion / TOM complex / regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein-transporting ATPase activity / branching involved in prostate gland morphogenesis / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Mitochondrial protein import / regulation of extrinsic apoptotic signaling pathway via death domain receptors / death receptor binding / protein targeting to mitochondrion / Cul2-RING ubiquitin ligase complex / protein import into mitochondrial matrix / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / sperm midpiece / PINK1-PRKN Mediated Mitophagy / cell periphery / unfolded protein binding / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / mitochondrial outer membrane / Ub-specific processing proteases / protein ubiquitination / apoptotic process / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM20 homolog / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsZhao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2025
Title: TOM20-driven E3 ligase recruitment regulates mitochondrial dynamics through PLD6.
Authors: Anat Raiff / Shidong Zhao / Aizat Bekturova / Colin Zenge / Shir Mazor / Xinyan Chen / Wenwen Ru / Yaara Makaros / Tslil Ast / Alban Ordureau / Chao Xu / Itay Koren /
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 ...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.
History
DepositionAug 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein fem-1 homolog B
C: Poly-UNK
B: Mitochondrial import receptor subunit TOM20 homolog


Theoretical massNumber of molelcules
Total (without water)84,9793
Polymers84,9793
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein fem-1 homolog B / FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic ...FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic pathway protein alpha / F1A-alpha


Mass: 70355.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1B, F1AA, KIAA0396 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UK73
#2: Protein/peptide Poly-UNK


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Mitochondrial import receptor subunit TOM20 homolog / Mitochondrial 20 kDa outer membrane protein / Outer mitochondrial membrane receptor Tom20


Mass: 13839.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM20, KIAA0016 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15388
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Local refinement of FEM1B bound with TOM20 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 55.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 222336 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045605
ELECTRON MICROSCOPYf_angle_d0.5617601
ELECTRON MICROSCOPYf_dihedral_angle_d4.331761
ELECTRON MICROSCOPYf_chiral_restr0.043881
ELECTRON MICROSCOPYf_plane_restr0.005991

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