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- EMDB-63187: local refinement of FEM1B bound with PLD6 -

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Basic information

Entry
Database: EMDB / ID: EMD-63187
Titlelocal refinement of FEM1B bound with PLD6
Map data
Sample
  • Complex: Local refinement of FEM1B bound with PLD6
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Mitochondrial cardiolipin hydrolase
Keywordsubiquitination E3 ligase / Cryo-EM / PROTEIN BINDING
Function / homology
Function and homology information


cardiolipin hydrolase activity / Synthesis of PG / P granule organization / regulation of ubiquitin-protein transferase activity / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / epithelial cell maturation involved in prostate gland development / Synthesis of PA / piRNA processing / positive regulation of mitochondrial fusion / branching involved in prostate gland morphogenesis ...cardiolipin hydrolase activity / Synthesis of PG / P granule organization / regulation of ubiquitin-protein transferase activity / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / epithelial cell maturation involved in prostate gland development / Synthesis of PA / piRNA processing / positive regulation of mitochondrial fusion / branching involved in prostate gland morphogenesis / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / 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 / mitochondrial outer membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsZhao S / Xu C
Funding support China, 1 items
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, 2025-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63187.png

Downloads & links

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Map

FileDownload / File: emd_63187.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.6320208 - 1.267095
Average (Standard dev.)0.000086737295 (±0.011855463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63187_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63187_half_map_2.map
Projections & Slices
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Sample components

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Entire : Local refinement of FEM1B bound with PLD6

EntireName: Local refinement of FEM1B bound with PLD6
Components
  • Complex: Local refinement of FEM1B bound with PLD6
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Mitochondrial cardiolipin hydrolase

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Supramolecule #1: Local refinement of FEM1B bound with PLD6

SupramoleculeName: Local refinement of FEM1B bound with PLD6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein fem-1 homolog B

MacromoleculeName: Protein fem-1 homolog B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.355062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEGLAGYVYK AASEGKVLTL AALLLNRSES DIRYLLGYVS QQGGQRSTPL IIAARNGHAK VVRLLLEHYR VQTQQTGTVR FDGYVIDGA TALWCAAGAG HFEVVKLLVS HGANVNHTTV TNSTPLRAAC FDGRLDIVKY LVENNANISI ANKYDNTCLM I AAYKGHTD ...String:
MEGLAGYVYK AASEGKVLTL AALLLNRSES DIRYLLGYVS QQGGQRSTPL IIAARNGHAK VVRLLLEHYR VQTQQTGTVR FDGYVIDGA TALWCAAGAG HFEVVKLLVS HGANVNHTTV TNSTPLRAAC FDGRLDIVKY LVENNANISI ANKYDNTCLM I AAYKGHTD VVRYLLEQRA DPNAKAHCGA TALHFAAEAG HIDIVKELIK WRAAIVVNGH GMTPLKVAAE SCKADVVELL LS HADCDRR SRIEALELLG ASFANDRENY DIIKTYHYLY LAMLERFQDG DNILEKEVLP PIHAYGNRTE CRNPQELESI RQD RDALHM EGLIVRERIL GADNIDVSHP IIYRGAVYAD NMEFEQCIKL WLHALHLRQK GNRNTHKDLL RFAQVFSQMI HLNE TVKAP DIECVLRCSV LEIEQSMNRV KNISDADVHN AMDNYECNLY TFLYLVCIST KTQCSEEDQC KINKQIYNLI HLDPR TREG FTLLHLAVNS NTPVDDFHTN DVCSFPNALV TKLLLDCGAE VNAVDNEGNS ALHIIVQYNR PISDFLTLHS IIISLV EAG AHTDMTNKQN KTPLDKSTTG VSEILLKTQM KMSLKCLAAR AVRANDINYQ DQIPRTLEEF VGFH

UniProtKB: Protein fem-1 homolog B

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Macromolecule #2: Mitochondrial cardiolipin hydrolase

MacromoleculeName: Mitochondrial cardiolipin hydrolase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.884283 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RPRREALFFP SQVTCTEALL RAPGAELAEL PEGCPCGLPH GESALSRLLR ALLAARASLD LCLFAFSSPQ LGRAVQLLHQ RGVRVRVVT DCDYMALNGS QIGLLRKAGI QVRHDQDPGY MHHKFAIVDK RVLITGSLNW TTQAIQNNRE NVLITEDDEY V RLFLEEFE ...String:
RPRREALFFP SQVTCTEALL RAPGAELAEL PEGCPCGLPH GESALSRLLR ALLAARASLD LCLFAFSSPQ LGRAVQLLHQ RGVRVRVVT DCDYMALNGS QIGLLRKAGI QVRHDQDPGY MHHKFAIVDK RVLITGSLNW TTQAIQNNRE NVLITEDDEY V RLFLEEFE RIWEQFNPTK YTFFPPKKSH GSCAPPVSRA GGRLLS

UniProtKB: Mitochondrial cardiolipin hydrolase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.8 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97465
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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