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- PDB-8u80: KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)... -

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Basic information

Entry
Database: PDB / ID: 8u80
TitleKCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)/Cullin3(NTD)
Components
  • BTB/POZ domain-containing protein KCTD5
  • Cullin-3
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 / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition ...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 / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / Notch binding / fibroblast apoptotic process / RHOBTB1 GTPase cycle / negative regulation of type I interferon production / stem cell division / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / negative regulation of Rho protein signal transduction / stress fiber assembly / positive regulation of cytokinesis / ubiquitin ligase complex scaffold activity / cullin family protein binding / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / sperm flagellum / RHOBTB2 GTPase cycle / protein K48-linked ubiquitination / 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 / integrin-mediated signaling pathway / cellular response to amino acid stimulus / Degradation of DVL / kidney development / G1/S transition of mitotic cell cycle / Hedgehog 'on' state / protein homooligomerization / protein destabilization / Wnt signaling pathway / protein polyubiquitination / Regulation of RAS by GAPs / spindle pole / mitotic spindle / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / gene expression / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynapse / protein ubiquitination / inflammatory response / positive regulation of cell population proliferation / ubiquitin protein ligase binding / centrosome / protein-containing complex binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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 alpha solenoid domain / Cullin family profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Cullin-3 / BTB/POZ domain-containing protein KCTD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKuntz, D.A. / Nguyen, D.M. / Narayanan, N. / Prive, G.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) 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
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
C1: Cullin-3
C2: Cullin-3
C3: Cullin-3
C4: Cullin-3
C5: Cullin-3


Theoretical massNumber of molelcules
Total (without water)353,30410
Polymers353,30410
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
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
#2: Protein
Cullin-3 / CUL-3


Mass: 44535.152 Da / Num. of mol.: 5
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

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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: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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 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
4cryoSPARCCTF correction
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64612 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 172.2 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00519570
ELECTRON MICROSCOPYf_angle_d0.649526335
ELECTRON MICROSCOPYf_chiral_restr0.03652905
ELECTRON MICROSCOPYf_plane_restr0.00473425
ELECTRON MICROSCOPYf_dihedral_angle_d5.15122615

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