+Open data
-Basic information
Entry | Database: PDB / ID: 8k8t | |||||||||||||||
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Title | Structure of CUL3-RBX1-KLHL22 complex | |||||||||||||||
Components |
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Keywords | LIGASE / Cullin Ring E3 ubiquitin ligase | |||||||||||||||
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 / stem cell division ...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 / stem cell division / RHOBTB3 ATPase cycle / cellular response to L-leucine / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / fibroblast apoptotic process / Notch binding / RHOBTB1 GTPase cycle / negative regulation of Rho protein signal transduction / mitotic metaphase chromosome alignment / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / intercellular bridge / stress fiber assembly / positive regulation of cytokinesis / mitotic spindle assembly checkpoint signaling / protein monoubiquitination / mitotic sister chromatid segregation / ubiquitin-like ligase-substrate adaptor activity / sperm flagellum / endoplasmic reticulum to Golgi vesicle-mediated transport / RHOBTB2 GTPase cycle / protein autoubiquitination / protein K48-linked ubiquitination / gastrulation / 14-3-3 protein binding / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of autophagy / cyclin binding / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / protein destabilization / Hedgehog 'on' state / mitotic spindle / Wnt signaling pathway / spindle pole / protein polyubiquitination / Regulation of RAS by GAPs / G1/S transition of mitotic cell cycle / microtubule cytoskeleton / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / positive regulation of cell growth / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynapse / Potential therapeutics for SARS / lysosome / protein ubiquitination / inflammatory response / cell division / intracellular membrane-bounded organelle / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
Authors | Wang, W. / Ling, L. / Dai, Z. / Zuo, P. / Yin, Y. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Nat Commun / Year: 2024 Title: A conserved N-terminal motif of CUL3 contributes to assembly and E3 ligase activity of CRL3. Authors: Weize Wang / Ling Liang / Zonglin Dai / Peng Zuo / Shang Yu / Yishuo Lu / Dian Ding / Hongyi Chen / Hui Shan / Yan Jin / Youdong Mao / Yuxin Yin / Abstract: The CUL3-RING E3 ubiquitin ligases (CRL3s) play an essential role in response to extracellular nutrition and stress stimuli. The ubiquitin ligase function of CRL3s is activated through dimerization. ...The CUL3-RING E3 ubiquitin ligases (CRL3s) play an essential role in response to extracellular nutrition and stress stimuli. The ubiquitin ligase function of CRL3s is activated through dimerization. However, how and why such a dimeric assembly is required for its ligase activity remains elusive. Here, we report the cryo-EM structure of the dimeric CRL3 complex and reveal a conserved N-terminal motif in CUL3 that contributes to the dimerization assembly and the E3 ligase activity of CRL3. We show that deletion of the CUL3 N-terminal motif impairs dimeric assembly and the E3 ligase activity of both CRL3 and several other CRL3s. In addition, we found that the dynamics of dimeric assembly of CRL3 generates a variable ubiquitination zone, potentially facilitating substrate recognition and ubiquitination. These findings demonstrate that a CUL3 N-terminal motif participates in the assembly process and provide insights into the assembly and activation of CRL3s. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k8t.cif.gz | 252.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k8t.ent.gz | 187.3 KB | Display | PDB format |
PDBx/mmJSON format | 8k8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k8t_validation.pdf.gz | 690.7 KB | Display | wwPDB validaton report |
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Full document | 8k8t_full_validation.pdf.gz | 716.7 KB | Display | |
Data in XML | 8k8t_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 8k8t_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/8k8t ftp://data.pdbj.org/pub/pdb/validation_reports/k8/8k8t | HTTPS FTP |
-Related structure data
Related structure data | 36961MC 8k9iC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 90134.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13618 #2: Protein | Mass: 74978.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: his-tev cleave site-klhl22 / Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL22 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q53GT1 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CUL3-RBX1-KLHL22 complex without CUL3 NA motif / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142416 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.32 Å2 | ||||||||||||||||||||||||
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