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- PDB-8u81: KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8u81 | ||||||
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Title | KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement Map | ||||||
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![]() | LIGASE / cullin family protein / proteasome-mediated ubiquitin-dependent protein catabolic process / complex / ubiquitin-dependent protein catabolic process | ||||||
Function / homology | ![]() 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 / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division ...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 / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / ubiquitin ligase complex scaffold activity / negative regulation of type I interferon production / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / protein monoubiquitination / positive regulation of cytokinesis / cullin family protein binding / sperm flagellum / protein K48-linked ubiquitination / RHOBTB2 GTPase cycle / protein autoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / gastrulation / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / cyclin binding / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / Olfactory Signaling Pathway / Activation of the phototransduction cascade / protein homooligomerization / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / 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 / mitotic spindle / Wnt signaling pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / spindle pole / 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 / sensory perception of taste / Regulation of RAS by GAPs / protein polyubiquitination / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / G1/S transition of mitotic cell cycle / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / G alpha (12/13) signalling events / extracellular vesicle / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor complex adaptor activity / cell migration / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / Neddylation / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / G alpha (i) signalling events / fibroblast proliferation / ubiquitin-dependent protein catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å | ||||||
![]() | Kuntz, D.A. / Nguyen, D.M. / Narayanan, N. / Prive, G.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and dynamics of a pentameric KCTD5/CUL3/Gβγ E3 ubiquitin ligase complex. Authors: Duc Minh Nguyen / Deanna H Rath / Dominic Devost / Darlaine Pétrin / Robert Rizk / Alan X Ji / Naveen Narayanan / Darren Yong / Andrew Zhai / Douglas A Kuntz / Maha U Q Mian / Neil C Pomroy ...Authors: Duc Minh Nguyen / Deanna H Rath / Dominic Devost / Darlaine Pétrin / Robert Rizk / Alan X Ji / Naveen Narayanan / Darren Yong / Andrew Zhai / Douglas A Kuntz / Maha U Q Mian / Neil C Pomroy / Alexander F A Keszei / Samir Benlekbir / Mohammad T Mazhab-Jafari / John L Rubinstein / Terence E Hébert / Gilbert G Privé / ![]() Abstract: Heterotrimeric G proteins can be regulated by posttranslational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C- ...Heterotrimeric G proteins can be regulated by posttranslational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain, engages CUL3 to form the central scaffold of a cullin-RING E3 ligase complex (CRL3) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3/Gβγ assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5/CUL3 and KCTD5/Gβγ moieties of the structure. CRL3 engages the E3 ligase ARIH1 to ubiquitylate Gβγ in an E3-E3 superassembly, and extension of the structure to include full-length CUL3 with RBX1 and an ARIH1~ubiquitin conjugate reveals that some conformational states position the ARIH1~ubiquitin thioester bond to within 10 Å of lysine-23 of Gβ and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3/Gβγ complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex. #1: ![]() Title: Structure and dynamics of a pentameric KCTD5/Cullin3/G beta gamma E3 ubiquitin ligase complex Authors: Nguyen, D.M. / Rath, D.H. / Devost, D. / Petrin, D. / Rizk, R. / Ji, A.X. / Narayanan, N. / Yong, D. / Zhai, A. / Kuntz, D.A. / Mian, M.U.Q. / Pomroy, N.C. / Keszei, A.F.E. / Benlekbir, S. / ...Authors: Nguyen, D.M. / Rath, D.H. / Devost, D. / Petrin, D. / Rizk, R. / Ji, A.X. / Narayanan, N. / Yong, D. / Zhai, A. / Kuntz, D.A. / Mian, M.U.Q. / Pomroy, N.C. / Keszei, A.F.E. / Benlekbir, S. / Mazhab-Jafari, M.T. / Rubinstein, J.L. / Hebert, T.E. / Prive, G.G. #2: ![]() Title: Structure and dynamics of a pentameric KCTD5/Cullin3/G beta gamma E3 ubiquitin ligase complex Authors: Nguyen, D.M. / Rath, D.H. / Devost, D. / Petrin, D. / Rizk, R. / Ji, A.X. / Narayanan, N. / Yong, D. / Zhai, A. / Kuntz, D.A. / Mian, M.U.Q. / Pomroy, N.C. / Keszei, A.F.E. / Benlekbir, S. / ...Authors: Nguyen, D.M. / Rath, D.H. / Devost, D. / Petrin, D. / Rizk, R. / Ji, A.X. / Narayanan, N. / Yong, D. / Zhai, A. / Kuntz, D.A. / Mian, M.U.Q. / Pomroy, N.C. / Keszei, A.F.E. / Benlekbir, S. / Mazhab-Jafari, M.T. / Rubinstein, J.L. / Hebert, T.E. / Prive, G.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 805.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 41996MC ![]() 8u7zC ![]() 8u80C ![]() 8u82C ![]() 8u83C ![]() 8u84C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 25994.367 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 44535.152 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 37416.930 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 7845.078 Da / Num. of mol.: 5 / Mutation: C68S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: KCTD5:Cullin3:GBetaGamma Pentamer / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: Human adenovirus 1 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 250 nm |
Image recording | Electron dose: 49.35 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 7464 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4103962 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48895 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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