+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35212 | |||||||||
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Title | Cryo-EM structure of KCTD7 in complex with Cullin3 | |||||||||
Map data | cryoEM map of KCTD7/CUL3 | |||||||||
Sample |
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Keywords | CUL3 / ubiquitination / E3 ligase / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / positive regulation of transporter activity / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating ...liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / positive regulation of transporter activity / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / intracellular potassium ion homeostasis / intracellular glutamate homeostasis / stem cell division / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / membrane hyperpolarization / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / sperm flagellum / protein autoubiquitination / protein K48-linked ubiquitination / RHOBTB2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / gastrulation / positive regulation of TORC1 signaling / cyclin binding / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / protein homooligomerization / G1/S transition of mitotic cell cycle / mitotic spindle / Wnt signaling pathway / spindle pole / Regulation of RAS by GAPs / protein polyubiquitination / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / protein ubiquitination / inflammatory response / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Jiang W / Wang W / Zheng S | |||||||||
Funding support | China, 1 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structural basis for the ubiquitination of G protein βγ subunits by KCTD5/Cullin3 E3 ligase. Authors: Wentong Jiang / Wei Wang / Yinfei Kong / Sanduo Zheng / Abstract: G protein-coupled receptor (GPCR) signaling is precisely controlled to avoid overstimulation that results in detrimental consequences. Gβγ signaling is negatively regulated by a Cullin3 (Cul3)- ...G protein-coupled receptor (GPCR) signaling is precisely controlled to avoid overstimulation that results in detrimental consequences. Gβγ signaling is negatively regulated by a Cullin3 (Cul3)-dependent E3 ligase, KCTD5, which triggers ubiquitination and degradation of free Gβγ. Here, we report the cryo-electron microscopy structures of the KCTD5-Gβγ fusion complex and the KCTD7-Cul3 complex. KCTD5 in pentameric form engages symmetrically with five copies of Gβγ through its C-terminal domain. The unique pentameric assembly of the KCTD5/Cul3 E3 ligase places the ubiquitin-conjugating enzyme (E2) and the modification sites of Gβγ in close proximity and allows simultaneous transfer of ubiquitin from E2 to five Gβγ subunits. Moreover, we show that ubiquitination of Gβγ by KCTD5 is important for fine-tuning cyclic adenosine 3´,5´-monophosphate signaling of GPCRs. Our studies provide unprecedented insights into mechanisms of substrate recognition by unusual pentameric E3 ligases and highlight the KCTD family as emerging regulators of GPCR signaling. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35212.map.gz | 51.5 MB | EMDB map data format | |
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Header (meta data) | emd-35212-v30.xml emd-35212.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
Images | emd_35212.png | 46.5 KB | ||
Others | emd_35212_additional_1.map.gz emd_35212_half_map_1.map.gz emd_35212_half_map_2.map.gz | 91.8 MB 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35212 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35212 | HTTPS FTP |
-Related structure data
Related structure data | 8i79MC 8jkbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35212.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | cryoEM map of KCTD7/CUL3 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: cryoEM map of KCTD7/CUL3 after map sharpening
File | emd_35212_additional_1.map | ||||||||||||
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Annotation | cryoEM map of KCTD7/CUL3 after map sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of KCTD7/CUL3
File | emd_35212_half_map_1.map | ||||||||||||
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Annotation | half map of KCTD7/CUL3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of KCTD7/CUL3
File | emd_35212_half_map_2.map | ||||||||||||
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Annotation | half map of KCTD7/CUL3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : complex of KCTD7 and Cullin-3
Entire | Name: complex of KCTD7 and Cullin-3 |
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Components |
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-Supramolecule #1: complex of KCTD7 and Cullin-3
Supramolecule | Name: complex of KCTD7 and Cullin-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #2: KCTD7
Supramolecule | Name: KCTD7 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Cullin-3
Supramolecule | Name: Cullin-3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: BTB/POZ domain-containing protein KCTD7
Macromolecule | Name: BTB/POZ domain-containing protein KCTD7 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 34.146633 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DYKDDDDKMV VVTGREPDSR HSDGAMSSSE AEDDFLEPAT PTATQAGHGL PLLPQEFPEV VPLNIGGAHF TTRLSTLRRY EDTMLAAMF SGRHYIPTDS EGRYFIDRDG THFGDVLNFL RSGDLPPREH VRAVYKEAQY YAIGPLLEQL ENMQPLKGEK V RQAFLGLM ...String: DYKDDDDKMV VVTGREPDSR HSDGAMSSSE AEDDFLEPAT PTATQAGHGL PLLPQEFPEV VPLNIGGAHF TTRLSTLRRY EDTMLAAMF SGRHYIPTDS EGRYFIDRDG THFGDVLNFL RSGDLPPREH VRAVYKEAQY YAIGPLLEQL ENMQPLKGEK V RQAFLGLM PYYKDHLERI VEIARLRAVQ RKARFAKLKV CVFKEEMPIT PYECPLLNSL RFERSESDGQ LFEHHCEVDV SF GPWEAVA DVYDLLHCLV TDLSAQGLTV DHQCIGVCDK HLVNHYYCKR PIYEFKITWW UniProtKB: BTB/POZ domain-containing protein KCTD7 |
-Macromolecule #2: Cullin-3
Macromolecule | Name: Cullin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.146426 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHGSP MTMDEKYVNS IWDLLKNAIQ EIQRKNNSGL SFEELYRNAY TMVLHKHGEK LYTGLREVVT EHLINKVRED VLNSLNNNF LQTLNQAWND HQTAMVMIRD ILMYMDRVYV QQNNVENVYN LGLIIFRDQV VRYGCIRDHL RQTLLDMIAR E RKGEVVDR ...String: MHHHHHHGSP MTMDEKYVNS IWDLLKNAIQ EIQRKNNSGL SFEELYRNAY TMVLHKHGEK LYTGLREVVT EHLINKVRED VLNSLNNNF LQTLNQAWND HQTAMVMIRD ILMYMDRVYV QQNNVENVYN LGLIIFRDQV VRYGCIRDHL RQTLLDMIAR E RKGEVVDR GAIRNACQML MILGLEGRSV YEEDFEAPFL EMSAEFFQME SQKFLAENSA SVYIKKVEAR INEEIERVMH CL DKSTEEP IVKVVERELI SKHMKTIVEM ENSGLVHMLK NGKTEDLGCM YKLFSRVPNG LKTMCECMSS YLREQGKALV SEE GEGKNP VDYRQGLDDL KSRFDRFLLE SFNNDRLFKQ TIAGDFEYFL NLNSRSPEYL UniProtKB: Cullin-3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.32 mg/mL | ||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.56 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 398489 |
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Startup model | Type of model: INSILICO MODEL |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cryoSPARC |
Final 3D classification | Number classes: 3 / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Number classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 115147 |