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- EMDB-61198: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer) -

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Entry
Database: EMDB / ID: EMD-61198
TitleCryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
Map data
Sample
  • Complex: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
    • Protein or peptide: Cullin-2
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
    • Protein or peptide: Poly-UNK
    • Protein or peptide: Poly-UNK
  • Ligand: ZINC ION
Keywordsubiquitination E3 ligase / Cryo-EM / PROTEIN BINDING
Function / homology
Function and homology information


tRNA import into mitochondrion / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein-transporting ATPase activity / migrasome / negative regulation of beige fat cell differentiation / mitochondria-associated endoplasmic reticulum membrane contact site / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity ...tRNA import into mitochondrion / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein-transporting ATPase activity / migrasome / negative regulation of beige fat cell differentiation / mitochondria-associated endoplasmic reticulum membrane contact site / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / negative regulation of mitophagy / cullin-RING ubiquitin ligase complex / regulation of xenophagy / Mitochondrial protein import / target-directed miRNA degradation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / elongin complex / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation of protein autoubiquitination / protein neddylation / regulation of BMP signaling pathway / NEDD8 ligase activity / : / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / protein K27-linked ubiquitination / VCB complex / Cul5-RING ubiquitin ligase complex / regulation of TOR signaling / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / regulation of mitotic cytokinesis / Cul3-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / negative regulation of type I interferon production / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / protein import into mitochondrial matrix / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / regulation of cellular response to stress / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / limb development / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / protein monoubiquitination / cullin family protein binding / Tat-mediated elongation of the HIV-1 transcript / ubiquitin ligase complex / Formation of HIV-1 elongation complex containing HIV-1 Tat / regulation of DNA-templated DNA replication initiation / centrosome duplication / Formation of HIV elongation complex in the absence of HIV Tat / cilium assembly / ubiquitin-like ligase-substrate adaptor activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / negative regulation of insulin receptor signaling pathway / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / post-translational protein modification / sperm midpiece / cellular response to amino acid stimulus / regulation of embryonic development / replication fork processing / transcription corepressor binding / negative regulation of canonical NF-kappaB signal transduction / rescue of stalled cytosolic ribosome / regulation of mitotic cell cycle / cell periphery / site of DNA damage / Regulation of BACH1 activity / T cell activation / PINK1-PRKN Mediated Mitophagy / TP53 Regulates Transcription of DNA Repair Genes
Similarity search - Function
Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Elongin-C / Elongin B / : / Cullin protein neddylation domain ...Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Elongin-C / Elongin B / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ankyrin repeat / SKP1/BTB/POZ domain superfamily / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-2 / Elongin-C / Elongin-B / Mitochondrial import receptor subunit TOM20 homolog / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 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: 2026
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 18, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61198.png

Downloads & links

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Map

FileDownload / File: emd_61198.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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 (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.24823381 - 0.6066203
Average (Standard dev.)0.0003574097 (±0.010797104)
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: #2

Fileemd_61198_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61198_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)

EntireName: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
Components
  • Complex: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
    • Protein or peptide: Cullin-2
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
    • Protein or peptide: Poly-UNK
    • Protein or peptide: Poly-UNK
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)

SupramoleculeName: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 / Details: CUL2-FEM1B BOUND WITH TOM20
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.11475 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SASWSHPQFE KGGGSGGGSG TSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHV RHLHKRVLES EEQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNGGG PLMEIGELAL DMWRKLMVEP L QAILIRML ...String:
SASWSHPQFE KGGGSGGGSG TSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHV RHLHKRVLES EEQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNGGG PLMEIGELAL DMWRKLMVEP L QAILIRML LREIKNDRGG EDPNQKVIHG VINSFVHVEQ YKKKFPLKFY QEIFESPFLT ETGEYYKQEA SNLLQESNCS QY MEKVLGR LKDEEIRCRK YLHPSSYTKV IHECQQRMVA DHLQFLHAEC HNIIRQEKKN DMANMYVLLR AVSTGLPHMI QEL QNHIHD EGLRATSNLT QENMPTLFVE SVLEVHGKFV QLINTVLNGD QHFMSALDKA LTSVVNYREP KSVCKAPELL AKYC DNLLK KSAKGMTENE VEDRLTSFIT VFKYIDDKDV FQKFYARMLA KRLIHGLSMS MDSEEAMINK LKQACGYEFT SKLHR MYTD MSVSADLNNK FNNFIKNQDT VIDLGISFQI YVLQAGAWPL TQAPSSTFAI PQELEKSVQM FELFYSQHFS GRKLTW LHY LCTGEVKMNY LGKPYVAMVT TYQMAVLLAF NNSETVSYKE LQDSTQMNEK ELTKTIKSLL DVKMINHDSE KEDIDAE SS FSLNMNFSSK RTKFKITTSM QKDTPQEMEQ TRSAVDEDRK MYLQAAIVRI MKARKVLRHN ALIQEVISQS RARFNPSI S MIKKCIEVLI DKQYIERSQA SADEYSYVA

UniProtKB: Cullin-2

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Macromolecule #2: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.84342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC

UniProtKB: Elongin-C

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Macromolecule #3: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.348964 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GGSMDVFLMI RRHKTTIFTD AKESSTVFEL KRIVEGILKR PPDEQRLYKD DQLLDDGKTL GECGFTSQTA RPQAPATVGL AFRADDTFE ALCIEPFSSP PELPDVMKPQ DSGSSANEQA VQ

UniProtKB: Elongin-B

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Macromolecule #4: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.19683 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SHMGAGKKRF EVKKWNAVAL WAWDIVVDNC AICRNHIMDL CIECQANQAS ATSEECTVAW GVCNHAFHFH CISRWLKTRQ VCPLDNREW EFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #5: Protein fem-1 homolog B

MacromoleculeName: Protein fem-1 homolog B / type: protein_or_peptide / ID: 5 / Number of copies: 4 / 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 #6: Mitochondrial import receptor subunit TOM20 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM20 homolog / type: protein_or_peptide / ID: 6 / Number of copies: 4 / 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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Macromolecule #7: Poly-UNK

MacromoleculeName: Poly-UNK / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 869.063 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #8: Poly-UNK

MacromoleculeName: Poly-UNK / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 698.854 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / 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
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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