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- PDB-9j78: Cryo-EM structure of CRL2-FEM1B (dimer 2) -

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Entry
Database: PDB / ID: 9j78
TitleCryo-EM structure of CRL2-FEM1B (dimer 2)
Components
  • (Poly-UNK) x 2
  • Cullin-2
  • E3 ubiquitin-protein ligase RBX1, N-terminally processed
  • Elongin-B
  • Elongin-C
  • Protein fem-1 homolog B
KeywordsPROTEIN BINDING / ubiquitination E3 ligase / Cryo-EM
Function / homology
Function and homology information


regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / branching involved in prostate gland morphogenesis / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / regulation of DNA damage checkpoint ...regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / branching involved in prostate gland morphogenesis / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / regulation of DNA damage checkpoint / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / target-directed miRNA degradation / elongin complex / regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of protein autoubiquitination / death receptor binding / RNA polymerase II transcription initiation surveillance / protein neddylation / NEDD8 ligase activity / protein K27-linked ubiquitination / negative regulation of response to oxidative stress / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Prolactin receptor signaling / Cul4-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cullin family protein binding / protein monoubiquitination / ubiquitin ligase complex / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / ubiquitin-like ligase-substrate adaptor activity / site of DNA damage / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / transcription-coupled nucleotide-excision repair / negative regulation of insulin receptor signaling pathway / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / post-translational protein modification / intrinsic apoptotic signaling pathway / T cell activation / transcription corepressor binding / Regulation of BACH1 activity / negative regulation of canonical NF-kappaB signal transduction / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / cellular response to amino acid stimulus / transcription elongation by RNA polymerase II / Degradation of DVL / Degradation of CRY and PER proteins / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Recognition of DNA damage by PCNA-containing replication complex / Hedgehog 'on' state / RING-type E3 ubiquitin transferase / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Inactivation of CSF3 (G-CSF) signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / Evasion by RSV of host interferon responses / DNA Damage Recognition in GG-NER / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Dual incision in TC-NER
Similarity search - Function
Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin, N-terminal / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin alpha solenoid domain / Cullin family signature. / Elongin-C / Elongin B ...Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin, N-terminal / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin alpha solenoid domain / Cullin family signature. / Elongin-C / Elongin B / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation 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 / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 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
H: Elongin-B
B: Cullin-2
C: Elongin-C
D: Elongin-B
J: Protein fem-1 homolog B
F: Protein fem-1 homolog B
A: Cullin-2
G: Elongin-C
E: E3 ubiquitin-protein ligase RBX1, N-terminally processed
I: E3 ubiquitin-protein ligase RBX1, N-terminally processed
K: Poly-UNK
L: Poly-UNK


Theoretical massNumber of molelcules
Total (without water)387,20112
Polymers387,20112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 10 molecules HDBACGJFEI

#1: 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
#2: 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
#3: 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
#4: 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.: 2
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
#5: 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

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Protein/peptide , 2 types, 2 molecules KL

#6: Protein/peptide Poly-UNK


Mass: 783.958 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)
#7: 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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Details

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 (dimer 2) / Type: COMPLEX / Details: Cryo-EM structure of CRL2-FEM1B (dimer 2) / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
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

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
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137665 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425670
ELECTRON MICROSCOPYf_angle_d0.61334688
ELECTRON MICROSCOPYf_dihedral_angle_d4.5893413
ELECTRON MICROSCOPYf_chiral_restr0.0433912
ELECTRON MICROSCOPYf_plane_restr0.0054454

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