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- EMDB-61362: local refinement of FEM1B bound with TOM20 -

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Basic information

Entry
Database: EMDB / ID: EMD-61362
Titlelocal refinement of FEM1B bound with TOM20
Map data
Sample
  • Complex: Local refinement of FEM1B bound with TOM20
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Poly-UNK
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
Keywordsubiquitination E3 ligase / Cryo-EM / PROTEIN BINDING
Function / homology
Function and homology information


tRNA import into mitochondrion / TOM complex / regulation of ubiquitin-protein transferase activity / mitochondrion targeting sequence binding / epithelial cell maturation involved in prostate gland development / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix ...tRNA import into mitochondrion / TOM complex / regulation of ubiquitin-protein transferase activity / mitochondrion targeting sequence binding / epithelial cell maturation involved in prostate gland development / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix / protein-transporting ATPase activity / branching involved in prostate gland morphogenesis / Mitochondrial protein import / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein targeting to mitochondrion / Cul2-RING ubiquitin ligase complex / response to muscle activity / protein insertion into mitochondrial outer membrane / 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 / cytosol / cytoplasm
Similarity search - Function
Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 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
DepositionAug 29, 2024-
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_61362.png

Downloads & links

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Map

FileDownload / File: emd_61362.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 640 pix.
= 524.8 Å		0.82 Å/pix.
x 640 pix.
= 524.8 Å		0.82 Å/pix.
x 640 pix.
= 524.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.9354848 - 1.4512525
Average (Standard dev.)0.0000012406343 (±0.012846375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 524.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61362_half_map_1.map
Projections & Slices
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Slices (1/2)
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Half map: #2

Fileemd_61362_half_map_2.map
Projections & Slices
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Sample components

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Entire : Local refinement of FEM1B bound with TOM20

EntireName: Local refinement of FEM1B bound with TOM20
Components
  • Complex: Local refinement of FEM1B bound with TOM20
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Poly-UNK
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog

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Supramolecule #1: Local refinement of FEM1B bound with TOM20

SupramoleculeName: Local refinement of FEM1B bound with TOM20 / 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: Poly-UNK

MacromoleculeName: Poly-UNK / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 783.958 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Mitochondrial import receptor subunit TOM20 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM20 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.839889 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DRKRRSDPNF KNRLRERRKK QKLAKERAGL SKLPDLKDAE AVQKFFLEEI QLGEELLAQG EYEKGVDHLT NAIAVCGQPQ QLLQVLQQT LPPPVFQMLL TKLPTISQRI VSAQSLAEDD VE

UniProtKB: Mitochondrial import receptor subunit TOM20 homolog

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.8 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 222336
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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