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- PDB-9lkx: local refinement of FEM1B bound with PLD6 -

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Basic information

Entry
Database: PDB / ID: 9lkx
Titlelocal refinement of FEM1B bound with PLD6
Components
  • Mitochondrial cardiolipin hydrolase
  • Protein fem-1 homolog B
KeywordsPROTEIN BINDING / ubiquitination E3 ligase / Cryo-EM
Function / homology
Function and homology information


cardiolipin hydrolase activity / Synthesis of PG / P granule organization / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / regulation of ubiquitin-protein transferase activity / Synthesis of PA / epithelial cell maturation involved in prostate gland development / piRNA processing / positive regulation of mitochondrial fusion / branching involved in prostate gland morphogenesis ...cardiolipin hydrolase activity / Synthesis of PG / P granule organization / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / regulation of ubiquitin-protein transferase activity / Synthesis of PA / epithelial cell maturation involved in prostate gland development / piRNA processing / positive regulation of mitochondrial fusion / branching involved in prostate gland morphogenesis / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of DNA damage checkpoint / regulation of extrinsic apoptotic signaling pathway via death domain receptors / death receptor binding / mitochondrial fusion / Cul2-RING ubiquitin ligase complex / PIWI-interacting RNA (piRNA) biogenesis / spermatid development / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / lipid catabolic process / meiotic cell cycle / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / mitochondrial outer membrane / protein ubiquitination / apoptotic process / Golgi apparatus / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...: / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / 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 cardiolipin hydrolase / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 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
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_DOI / _citation.title / _em_admin.last_update
Revision 1.2May 7, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
J: Protein fem-1 homolog B
K: Mitochondrial cardiolipin hydrolase


Theoretical massNumber of molelcules
Total (without water)93,2392
Polymers93,2392
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 Mitochondrial cardiolipin hydrolase / Choline phosphatase 6 / Mitochondrial phospholipase / MitoPLD / Phosphatidylcholine-hydrolyzing ...Choline phosphatase 6 / Mitochondrial phospholipase / MitoPLD / Phosphatidylcholine-hydrolyzing phospholipase D6 / Phospholipase D6 / PLD6 / Protein zucchini homolog


Mass: 22884.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLD6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N2A8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
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 PLD6 / 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

MicroscopyModel: FEI MORGAGNI
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: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97465 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035198
ELECTRON MICROSCOPYf_angle_d0.627046
ELECTRON MICROSCOPYf_dihedral_angle_d4.713708
ELECTRON MICROSCOPYf_chiral_restr0.042809
ELECTRON MICROSCOPYf_plane_restr0.004916

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