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- PDB-8u83: KCTD5/Cullin3/Gbeta1gamma2 Complex: State C From Composite RELION... -

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Basic information

Entry
Database: PDB / ID: 8u83
TitleKCTD5/Cullin3/Gbeta1gamma2 Complex: State C From Composite RELION Multi-body Refinement Map
Components
  • BTB/POZ domain-containing protein KCTD5
  • Cullin-3
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
KeywordsLIGASE / cullin family protein / proteasome-mediated ubiquitin-dependent protein catabolic process / complex / ubiquitin-dependent protein catabolic process
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / embryonic cleavage / regulation protein catabolic process at postsynapse ...positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / embryonic cleavage / regulation protein catabolic process at postsynapse / RHOBTB3 ATPase cycle / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / stem cell division / Notch binding / fibroblast apoptotic process / RHOBTB1 GTPase cycle / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / mitotic metaphase chromosome alignment / ubiquitin ligase complex scaffold activity / stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of cytokinesis / cullin family protein binding / sperm flagellum / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / protein K48-linked ubiquitination / RHOBTB2 GTPase cycle / protein autoubiquitination / gastrulation / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / cyclin binding / positive regulation of protein ubiquitination / kidney development / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / protein homooligomerization / Wnt signaling pathway / mitotic spindle / Olfactory Signaling Pathway / Activation of the phototransduction cascade / spindle pole / 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 / G1/S transition of mitotic cell cycle / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Regulation of RAS by GAPs / photoreceptor disc membrane / Glucagon-type ligand receptors / protein polyubiquitination / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cell migration / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / Antigen processing: Ubiquitination & Proteasome degradation / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / Neddylation / GTPase binding / Ca2+ pathway / retina development in camera-type eye / ubiquitin-dependent protein catabolic process / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cellular response to oxidative stress / fibroblast proliferation
Similarity search - Function
Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin ...Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / 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. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Cullin-3 / BTB/POZ domain-containing protein KCTD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.975 Å
AuthorsKuntz, D.A. / Nguyen, D.M. / Narayanan, N. / Prive, G.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2024
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: Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
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: Journal: Biorxiv / Year: 2023
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
DepositionSep 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID / _audit_author.name
Revision 1.2Apr 24, 2024Group: Database references / Category: citation / citation_author
Revision 1.3May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B1: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B5: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C1: Cullin-3
C2: Cullin-3
C3: Cullin-3
C4: Cullin-3
C5: Cullin-3
G1: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G2: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
K1: BTB/POZ domain-containing protein KCTD5
K2: BTB/POZ domain-containing protein KCTD5
K3: BTB/POZ domain-containing protein KCTD5
K4: BTB/POZ domain-containing protein KCTD5
K5: BTB/POZ domain-containing protein KCTD5


Theoretical massNumber of molelcules
Total (without water)579,61420
Polymers579,61420
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37416.930 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P62873
#2: Protein
Cullin-3 / CUL-3


Mass: 44535.152 Da / Num. of mol.: 5 / Fragment: UNP residues 1-381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13618
#3: Protein
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7845.078 Da / Num. of mol.: 5 / Mutation: C68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P59768
#4: Protein
BTB/POZ domain-containing protein KCTD5


Mass: 26125.562 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NXV2

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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: pentameric KCTD5/Cullin3/GBetaGamma E3 ubiquitin ligase complex
Type: COMPLEX / Entity ID: #4, #2, #1, #3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 magnification: 75000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 250 nm
Image recordingElectron 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
IDNameCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
9ISOLDEmodel fitting
14RELION3D reconstruction
15PHENIXmodel refinement
16VMDmodel refinement
17NAMDmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.975 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48895 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDChain residue rangeInitial refinement model-IDPdb chain residue range
13DRX

3drx

C3DRXC35-211135-211
24EOZ

4eoz

B4EOZB24-325224-325
36VMS

6vms

B6VMSB2-34032-340
46VMS

6vms

C6VMSC6-6436-64

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