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- EMDB-61197: Cryo-EM structure of CRL2-FEM1B (dimer 2) -

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Entry
Database: EMDB / ID: EMD-61197
TitleCryo-EM structure of CRL2-FEM1B (dimer 2)
Map data
Sample
  • Complex: Cryo-EM structure of CRL2-FEM1B (dimer 2)
    • Protein or peptide: Elongin-B
    • Protein or peptide: Cullin-2
    • Protein or peptide: Elongin-C
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Poly-UNK
    • Protein or peptide: Poly-UNK
Keywordsubiquitination E3 ligase / Cryo-EM / PROTEIN BINDING
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 / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / regulation of DNA damage checkpoint / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway ...regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / branching involved in prostate gland morphogenesis / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / regulation of DNA damage checkpoint / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / VCB complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / elongin complex / positive regulation of protein autoubiquitination / death receptor binding / protein neddylation / regulation of extrinsic apoptotic signaling pathway via death domain receptors / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / cullin family protein binding / 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 / protein monoubiquitination / ubiquitin ligase complex / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / protein K48-linked ubiquitination / RNA Polymerase II Transcription Elongation / Nuclear events stimulated by ALK signaling in cancer / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / post-translational protein modification / intrinsic apoptotic signaling pathway / T cell activation / Regulation of BACH1 activity / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / cellular response to amino acid stimulus / Degradation of DVL / transcription elongation by RNA polymerase II / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Inactivation of CSF3 (G-CSF) signaling / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / NOTCH1 Intracellular Domain Regulates Transcription / Formation of TC-NER Pre-Incision Complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin / Dual incision in TC-NER / Regulation of RAS by GAPs / protein polyubiquitination / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / cellular response to UV / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation
Similarity search - Function
Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Elongin-C / Cullin family signature. / Elongin B / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain ...Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Elongin-C / Cullin family signature. / Elongin B / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / 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 repeats (3 copies) / Ankyrin repeat profile. / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 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 18, 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_61197.png

Downloads & links

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Map

FileDownload / File: emd_61197.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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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
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.37378863 - 0.72592384
Average (Standard dev.)0.00028667974 (±0.01070005)
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_61197_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61197_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of CRL2-FEM1B (dimer 2)

EntireName: Cryo-EM structure of CRL2-FEM1B (dimer 2)
Components
  • Complex: Cryo-EM structure of CRL2-FEM1B (dimer 2)
    • Protein or peptide: Elongin-B
    • Protein or peptide: Cullin-2
    • Protein or peptide: Elongin-C
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Poly-UNK
    • Protein or peptide: Poly-UNK

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Supramolecule #1: Cryo-EM structure of CRL2-FEM1B (dimer 2)

SupramoleculeName: Cryo-EM structure of CRL2-FEM1B (dimer 2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cryo-EM structure of CRL2-FEM1B (dimer 2)
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 1 / 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 #2: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 2 / 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 #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / 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 #4: Protein fem-1 homolog B

MacromoleculeName: Protein fem-1 homolog B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / 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 #5: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 5 / 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 #6: Poly-UNK

MacromoleculeName: Poly-UNK / type: protein_or_peptide / ID: 6 / 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 #7: Poly-UNK

MacromoleculeName: Poly-UNK / type: protein_or_peptide / ID: 7 / 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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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
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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137665
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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