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Yorodumi- EMDB-41995: KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(BTB... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41995 | |||||||||
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Title | KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(BTB)/Cullin3(NTD) | |||||||||
Map data | KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom: 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 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 / protein destabilization / protein homooligomerization / mitotic spindle / Wnt signaling pathway / spindle pole / protein polyubiquitination / Regulation of RAS by GAPs / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / gene expression / Neddylation / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / protein ubiquitination / inflammatory response / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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_41995.map.gz | 121.1 MB | EMDB map data format | |
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Header (meta data) | emd-41995-v30.xml emd-41995.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41995_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_41995.png | 103 KB | ||
Masks | emd_41995_msk_1.map | 129.7 MB | Mask map | |
Filedesc metadata | emd-41995.cif.gz | 4.6 KB | ||
Others | emd_41995_additional_1.map.gz emd_41995_half_map_1.map.gz emd_41995_half_map_2.map.gz | 64.2 MB 120.3 MB 120.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41995 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41995 | HTTPS FTP |
-Related structure data
Related structure data | 8u80MC 8u7zC 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_41995.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 Bottom: 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_41995_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom Sharpened
File | emd_41995_additional_1.map | ||||||||||||
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Annotation | KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom Sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom: HalfMap2
File | emd_41995_half_map_1.map | ||||||||||||
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Annotation | KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom: HalfMap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom Half Map 1
File | emd_41995_half_map_2.map | ||||||||||||
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Annotation | KCTD5:Cullin3:GBetaGamma Complex High Resolution Bottom Half Map 1 | ||||||||||||
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 |
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Source (natural) | Organism: Homo sapiens (human) |
-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-8u80: |