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Yorodumi- EMDB-41994: KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(CTD... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41994 | |||||||||
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Title | KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(CTD)/Gbeta1gamma2 | |||||||||
Map data | KCTD5:Cullin3:GBetaGamma Complex High Resolution Top: Full Map | |||||||||
Sample |
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Keywords | cullin family protein / proteasome-mediated ubiquitin-dependent protein catabolic process / complex / ubiquitin-dependent protein catabolic process / CYTOSOLIC PROTEIN | |||||||||
Function / homology | Function and homology information Cul3-RING ubiquitin ligase complex / cullin family protein binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / 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 ...Cul3-RING ubiquitin ligase complex / cullin family protein binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / 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 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / 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 / 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 / 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 / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Nguyen DM / Narayanan N / Kuntz DA / Prive GG | |||||||||
Funding support | Canada, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41994.map.gz | 64.2 MB | EMDB map data format | |
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Header (meta data) | emd-41994-v30.xml emd-41994.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41994_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_41994.png | 144 KB | ||
Masks | emd_41994_msk_1.map | 129.7 MB | Mask map | |
Filedesc metadata | emd-41994.cif.gz | 5.8 KB | ||
Others | emd_41994_additional_1.map.gz emd_41994_half_map_1.map.gz emd_41994_half_map_2.map.gz | 120.8 MB 120.4 MB 120.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41994 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41994 | HTTPS FTP |
-Related structure data
Related structure data | 8u7zMC 8u80C 8u81C 8u82C 8u83C 8u84C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41994.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | KCTD5:Cullin3:GBetaGamma Complex High Resolution Top: Full Map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41994_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Top: Sharpened Map used...
File | emd_41994_additional_1.map | ||||||||||||
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Annotation | KCTD5:Cullin3:GBetaGamma Complex High Resolution Top: Sharpened Map used for fitting | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Top: Half Map 1
File | emd_41994_half_map_1.map | ||||||||||||
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Annotation | KCTD5:Cullin3:GBetaGamma Complex High Resolution Top: Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Top: Half Map 2
File | emd_41994_half_map_2.map | ||||||||||||
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Annotation | KCTD5:Cullin3:GBetaGamma Complex High Resolution Top: Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gb...
Entire | Name: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma |
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Components |
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-Supramolecule #1: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gb...
Supramolecule | Name: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: KCTD5_HUMAN
Macromolecule | Name: KCTD5_HUMAN / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: GBB1_HUMAN
Macromolecule | Name: GBB1_HUMAN / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: GBG2_HUMAN
Macromolecule | Name: GBG2_HUMAN / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSA IL UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 recording | Film 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 |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8u7z: |