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- EMDB-41995: KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(BTB... -

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Basic information

Entry
Database: EMDB / ID: EMD-41995
TitleKCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(BTB)/Cullin3(NTD)
Map dataKCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom: Full Map
Sample
  • Complex: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma
Keywordscullin family protein / proteasome-mediated ubiquitin-dependent protein catabolic process / complex / ubiquitin-dependent protein catabolic process / CYTOSOLIC PROTEIN
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 / RHOBTB3 ATPase cycle ...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 / RHOBTB3 ATPase cycle / positive regulation of mitotic metaphase/anaphase transition / 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 / cytoplasm / cytosol
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsNguyen DM / Narayanan N / Kuntz DA / Prive GG
Funding support Canada, 1 items
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: Biorxiv / Year: 2023
Title: Structure and dynamics of a pentameric KCTD5/Cullin3/G beta gamma E3 ubiquitin ligase complex
Authors: Nguyen DM / Rath DH / Devost D / Petrin D / Rizk R / Ji AX / Narayanan N / Yong D / Zhai A / Kuntz DA / Mian MUQ / Pomroy NC / Keszei AFE / Benlekbir S / Mazhab-Jafari MT / Rubinstein JL / Hebert TE / Prive GG
History
DepositionSep 15, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41995.png

Downloads & links

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Map

FileDownload / File: emd_41995.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom: Full Map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 324 pix.
= 333.72 Å		1.03 Å/pix.
x 324 pix.
= 333.72 Å		1.03 Å/pix.
x 324 pix.
= 333.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0006409676 - 1.963374
Average (Standard dev.)0.0021220066 (±0.031378757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 333.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41995_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom Sharpened

Fileemd_41995_additional_1.map
AnnotationKCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom Sharpened
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom: HalfMap2

Fileemd_41995_half_map_1.map
AnnotationKCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom: HalfMap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom Half Map 1

Fileemd_41995_half_map_2.map
AnnotationKCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gb...

EntireName: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma
Components
  • Complex: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma

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Supramolecule #1: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gb...

SupramoleculeName: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 7464 / Average electron dose: 49.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 75000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4103962
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 64612
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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