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- PDB-9j79: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer) -

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Entry
Database: PDB / ID: 9j79
TitleCryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
Components
  • (Poly-UNK) x 2
  • Cullin-2
  • E3 ubiquitin-protein ligase RBX1, N-terminally processed
  • Elongin-B
  • Elongin-C
  • Mitochondrial import receptor subunit TOM20 homolog
  • Protein fem-1 homolog B
KeywordsPROTEIN BINDING / ubiquitination E3 ligase / Cryo-EM
Function / homology
Function and homology information


tRNA import into mitochondrion / TOM complex / response to 3,3',5-triiodo-L-thyronine / mitochondrial outer membrane translocase complex / mitochondrion targeting sequence binding / protein insertion into mitochondrial outer membrane / migrasome / negative regulation of beige fat cell differentiation / mitochondria-associated endoplasmic reticulum membrane contact site / cullin-RING-type E3 NEDD8 transferase ...tRNA import into mitochondrion / TOM complex / response to 3,3',5-triiodo-L-thyronine / mitochondrial outer membrane translocase complex / mitochondrion targeting sequence binding / protein insertion into mitochondrial outer membrane / migrasome / negative regulation of beige fat cell differentiation / mitochondria-associated endoplasmic reticulum membrane contact site / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy / Mitochondrial protein import / target-directed miRNA degradation / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / elongin complex / VCB complex / death receptor binding / regulation of cell cycle process / regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / positive regulation of cilium assembly / Cul5-RING ubiquitin ligase complex / response to muscle activity / ubiquitin-ubiquitin ligase activity / regulation of TOR signaling / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / SCF ubiquitin ligase complex / regulation of DNA damage checkpoint / regulation of mitotic cytokinesis / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / regulation of miRNA-mediated gene silencing / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of natural killer cell activation / protein import into mitochondrial matrix / Prolactin receptor signaling / nucleotide-excision repair complex / Cul4-RING E3 ubiquitin ligase complex / regulation of cell cycle phase transition / regulation of stem cell population maintenance / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Cul4B-RING E3 ubiquitin ligase complex / regulation of cellular response to stress / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / limb development / protein localization to mitochondrion / Cul4A-RING E3 ubiquitin ligase complex / transmembrane protein transporter activity / protein monoubiquitination / cullin family protein binding / protein targeting / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / centrosome duplication / Formation of HIV elongation complex in the absence of HIV Tat / regulation of DNA-templated DNA replication initiation / cilium assembly / RNA Polymerase II Transcription Elongation / ubiquitin-like ligase-substrate adaptor activity / Formation of RNA Pol II elongation complex / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / negative regulation of insulin receptor signaling pathway / signal transduction in response to DNA damage / ubiquitin ligase complex / protein K63-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / protein K48-linked ubiquitination / post-translational protein modification / positive regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / sperm midpiece / regulation of embryonic development / replication fork processing / cellular response to amino acid stimulus / transcription corepressor binding / regulation of mitotic cell cycle / negative regulation of canonical NF-kappaB signal transduction
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsZhao, S. / Xu, C.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Cullin-2
F: Elongin-C
H: Elongin-B
I: E3 ubiquitin-protein ligase RBX1, N-terminally processed
K: Cullin-2
L: Elongin-C
M: Elongin-B
N: E3 ubiquitin-protein ligase RBX1, N-terminally processed
J: Protein fem-1 homolog B
A: Protein fem-1 homolog B
B: Mitochondrial import receptor subunit TOM20 homolog
G: Mitochondrial import receptor subunit TOM20 homolog
D: Poly-UNK
O: Protein fem-1 homolog B
P: Protein fem-1 homolog B
S: Mitochondrial import receptor subunit TOM20 homolog
C: Mitochondrial import receptor subunit TOM20 homolog
Q: Poly-UNK
R: Poly-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)584,61725
Polymers584,22519
Non-polymers3926
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

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Protein , 6 types, 16 molecules EKFLHMINJAOPBGSC

#1: Protein Cullin-2 / CUL-2


Mass: 87114.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13617
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#3: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 13348.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#4: Protein E3 ubiquitin-protein ligase RBX1, N-terminally processed / E3 ubiquitin-protein transferase RBX1 / N-terminally processed


Mass: 11196.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62877
#5: 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.: 4
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
#6: 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.: 4
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

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Protein/peptide , 2 types, 3 molecules DRQ

#7: Protein/peptide Poly-UNK


Mass: 869.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#8: Protein/peptide Poly-UNK


Mass: 698.854 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)

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Non-polymers , 1 types, 6 molecules

#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
Type: COMPLEX / Details: CUL2-FEM1B BOUND WITH TOM20 / Entity ID: #1-#8 / 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
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
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
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 55.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92948 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00237390
ELECTRON MICROSCOPYf_angle_d0.55850619
ELECTRON MICROSCOPYf_dihedral_angle_d4.4955057
ELECTRON MICROSCOPYf_chiral_restr0.045767
ELECTRON MICROSCOPYf_plane_restr0.0046547

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