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- EMDB-42001: KCTD5/Cullin3/Gbeta1gamma2 Complex State B: Reference Map for Com... -

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Basic information

Entry
Database: EMDB / ID: EMD-42001
TitleKCTD5/Cullin3/Gbeta1gamma2 Complex State B: Reference Map for Composite Map EMD-42000
Map dataKCTD5:Cullin3:GBetaGamma StateB Relion Ref3D :Reference map for Multibody Composite Map Full map
Sample
  • Complex: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma
    • Protein or peptide: KCTD5_HUMAN
    • Protein or peptide: cullin3 1-381
    • Protein or peptide: GBB1_HUMAN
    • Protein or peptide: GBG2_HUMAN
Keywordscullin family protein / proteasome-mediated ubiquitin-dependent protein catabolic process / complex / ubiquitin-dependent protein catabolic process / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


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 / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition ...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 / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / stem cell division / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / cullin family protein binding / gastrulation / protein K48-linked ubiquitination / sperm flagellum / endoplasmic reticulum to Golgi vesicle-mediated transport / protein autoubiquitination / RHOBTB2 GTPase cycle / positive regulation of TORC1 signaling / cyclin binding / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / Olfactory Signaling Pathway / Activation of the phototransduction cascade / protein destabilization / 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 / mitotic spindle / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Wnt signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / spindle pole / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / protein polyubiquitination / 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 / Regulation of RAS by GAPs / 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 / ubiquitin protein ligase activity / G alpha (12/13) signalling events / KEAP1-NFE2L2 pathway / cell migration / signaling receptor complex adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / gene expression / phospholipase C-activating G protein-coupled receptor signaling pathway / Neddylation / G alpha (i) signalling events / fibroblast proliferation / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events
Similarity search - Function
Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / 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 / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / 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. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 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.USA / Year: 2024
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
#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-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42001.png

Downloads & links

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Map

FileDownload / File: emd_42001.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKCTD5:Cullin3:GBetaGamma StateB Relion Ref3D :Reference map for Multibody Composite Map Full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
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: 0.005
Minimum - Maximum-0.019106578 - 0.07831146
Average (Standard dev.)0.00011721885 (±0.0031239574)
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_42001_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: KCTD5:Cullin3:GBetaGamma StateB Relion Ref3D :Reference map for Multibody...

Fileemd_42001_half_map_1.map
AnnotationKCTD5:Cullin3:GBetaGamma StateB Relion Ref3D :Reference map for Multibody Composite Map Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: KCTD5:Cullin3:GBetaGamma StateB Relion Ref3D :Reference map for Multibody...

Fileemd_42001_half_map_2.map
AnnotationKCTD5:Cullin3:GBetaGamma StateB Relion Ref3D :Reference map for Multibody Composite Map Halmap 2
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
    • Protein or peptide: KCTD5_HUMAN
    • Protein or peptide: cullin3 1-381
    • Protein or peptide: GBB1_HUMAN
    • Protein or peptide: GBG2_HUMAN

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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 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: KCTD5_HUMAN

MacromoleculeName: KCTD5_HUMAN / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AENHCELLSP ARGGIGAGLG GGLCRRCSAG LGALAQRPGS VSKWVRLNVG GTYFLTTRQ TLCRDPKSFL YRLCQADPDL DSDKDETGAY LIDRDPTYFG PVLNYLRHGK LVINKDLAEE GVLEEAEFY NITSLIKLVK DKIRERDSKT SQVPVKHVYR VLQCQEEELT ...String:
AENHCELLSP ARGGIGAGLG GGLCRRCSAG LGALAQRPGS VSKWVRLNVG GTYFLTTRQ TLCRDPKSFL YRLCQADPDL DSDKDETGAY LIDRDPTYFG PVLNYLRHGK LVINKDLAEE GVLEEAEFY NITSLIKLVK DKIRERDSKT SQVPVKHVYR VLQCQEEELT QMVSTMSDGW K FEQLVSIG SSYNYGNEDQ AEFLCVVSKE LHNTPYGTAS EPSEKAKILQ ERGSRM

UniProtKB: BTB/POZ domain-containing protein KCTD5

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Macromolecule #2: cullin3 1-381

MacromoleculeName: cullin3 1-381 / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKVR EDVLNSLNNN FLQTLNQAWN DHQTAMVMIR DILMYMDRVY VQQNNVENVY NLGLIIFRDQ VVRYGCIRDH LRQTLLDMIA ...String:
MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKVR EDVLNSLNNN FLQTLNQAWN DHQTAMVMIR DILMYMDRVY VQQNNVENVY NLGLIIFRDQ VVRYGCIRDH LRQTLLDMIA RERKGEVVDR GAIRNACQML MILGLEGRSV YEEDFEAPFL EMSAEFFQME SQKFLAENSA SVYIKKVEAR INEEIERVMH CLDKSTEEPI VKVVERELIS KHMKTIVEME NSGLVHMLKN GKTEDLGCMY KLFSRVPNGL KTMCECMSSY LREQGKALVS EEGEGKNPVD YIQGLLDLKS RFDRFLLESF NNDRLFKQTI AGDFEYFLNL N

UniProtKB: Cullin-3

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Macromolecule #3: GBB1_HUMAN

MacromoleculeName: GBB1_HUMAN / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRL LVSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN I CSIYNLKT REGNVRVSRE LAGHTGYLSC CRFLDDNQIV TSSGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRL LVSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN I CSIYNLKT REGNVRVSRE LAGHTGYLSC CRFLDDNQIV TSSGDTTCAL WDIETGQQTT TF TGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DINAICFFPN GNA FATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDAL KADRA GVLAGHDNRV SCLGVTDDGM AVATGSWDSF LKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #4: GBG2_HUMAN

MacromoleculeName: GBG2_HUMAN / type: protein_or_peptide / ID: 4 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSA IL

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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

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Image processing

Particle selectionNumber selected: 4103962
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 48895
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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