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Yorodumi- EMDB-36367: Cryo-EM structure of KCTD5 in complex with Gbeta gamma subunits -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36367 | |||||||||
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Title | Cryo-EM structure of KCTD5 in complex with Gbeta gamma subunits | |||||||||
Map data | EM density map of KCTD5_Gng2/Gnb1 complex | |||||||||
Sample |
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Keywords | ubiquitination / GPCR signaling / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information Cul3-RING ubiquitin ligase complex / cullin family protein binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / protein homooligomerization / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway ...Cul3-RING ubiquitin ligase complex / cullin family protein binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / protein homooligomerization / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / 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: 3.27 Å | |||||||||
Authors | Zheng S / Jiang W / Wang W / Kong Y | |||||||||
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_36367.map.gz | 80.4 MB | EMDB map data format | |
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Header (meta data) | emd-36367-v30.xml emd-36367.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
Images | emd_36367.png | 58 KB | ||
Others | emd_36367_additional_1.map.gz emd_36367_half_map_1.map.gz emd_36367_half_map_2.map.gz | 154 MB 151.6 MB 151.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36367 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36367 | HTTPS FTP |
-Related structure data
Related structure data | 8jkbMC 8i79C 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_36367.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | EM density map of KCTD5_Gng2/Gnb1 complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: EM density map of KCTD5 Gng2/Gnb1 complex after sharpening
File | emd_36367_additional_1.map | ||||||||||||
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Annotation | EM density map of KCTD5_Gng2/Gnb1 complex after sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of KCTD5 Gng2/Gnb1 complex
File | emd_36367_half_map_1.map | ||||||||||||
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Annotation | half map of KCTD5_Gng2/Gnb1 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of KCTD5 Gng2/Gnb1 complex
File | emd_36367_half_map_2.map | ||||||||||||
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Annotation | half map of KCTD5_Gng2/Gnb1 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of KCTD5 in complex with G protein betagamma su...
Entire | Name: Cryo-EM structure of KCTD5 in complex with G protein betagamma subunits |
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Components |
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-Supramolecule #1: Cryo-EM structure of KCTD5 in complex with G protein betagamma su...
Supramolecule | Name: Cryo-EM structure of KCTD5 in complex with G protein betagamma subunits type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.088762 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MYPYDVPDYA YPYDVPDYAY PYDVPDYAGS GSMSELDQLR QEAEQLKNQI RDARKACADA TLSQITNNID PVGRIQMRTR RTLRGHLAK IYAMHWGTDS RLLVSASQDG KLIIWDSYTT NKVHAIPLRS SWVMTCAYAP SGNYVACGGL DNICSIYNLK T REGNVRVS ...String: MYPYDVPDYA YPYDVPDYAY PYDVPDYAGS GSMSELDQLR QEAEQLKNQI RDARKACADA TLSQITNNID PVGRIQMRTR RTLRGHLAK IYAMHWGTDS RLLVSASQDG KLIIWDSYTT NKVHAIPLRS SWVMTCAYAP SGNYVACGGL DNICSIYNLK T REGNVRVS RELAGHTGYL SCCRFLDDNQ IVTSSGDTTC ALWDIETGQQ TTTFTGHTGD VMSLSLAPDT RLFVSGACDA SA KLWDVRE GMCRQTFTGH ESDINAICFF PNGNAFATGS DDATCRLFDL RADQELMTYS HDNIICGITS VSFSKSGRLL LAG YDDFNC NVWDALKADR AGVLAGHDNR VSCLGVTDDG MAVATGSWDS FLKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 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: 10.228731 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GSALEVLFQG PGAGALEVLF QGPGSMASNN TASIAQARKL VEQLKMEANI DRIKVSKAAA DLMAYCEAHA KEDPLLTPVP ASENPFREK KFFSAIL UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #3: BTB/POZ domain-containing protein KCTD5
Macromolecule | Name: BTB/POZ domain-containing protein KCTD5 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 30.780623 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGSSHHHHHH GSEDQVDPRL IDGKDYKDDD DKLEVLFQGP MAENHCELLP PAPSGLGAGL GGGLCRRCSA GMGALAQRPG GVSKWVRLN VGGTYFLTTR QTLCRDPKSF LYRLCQADPD LDSDKDETGA YLIDRDPTYF GPVLNYLRHG KLVINKDLAE E GVLEEAEF ...String: MGSSHHHHHH GSEDQVDPRL IDGKDYKDDD DKLEVLFQGP MAENHCELLP PAPSGLGAGL GGGLCRRCSA GMGALAQRPG GVSKWVRLN VGGTYFLTTR QTLCRDPKSF LYRLCQADPD LDSDKDETGA YLIDRDPTYF GPVLNYLRHG KLVINKDLAE E GVLEEAEF YNITSLIKLV KDKIRERDSR ISQMPVKHVY RVLQCQEEEL TQMVSTMSDG WKFEQLVSIG SSYNYGNEDQ AE FLCVVSK ELHNTPYGTT SEPSEKAKIL QERGSRM UniProtKB: BTB/POZ domain-containing protein KCTD5 |
-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 | Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. | |||||||||
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: 2.6 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.71 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 2484234 |
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Startup model | Type of model: INSILICO MODEL |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final 3D classification | Number classes: 10 / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99265 |