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Open data
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Basic information
Entry | Database: PDB / ID: 8wqi | ||||||
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Title | Local refinement of FEM1B bound with the C-degron of CUX1 | ||||||
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![]() | PROTEIN BINDING / E3 ubiquitin ligase / Pro/C-degron | ||||||
Function / homology | ![]() regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / Intra-Golgi traffic / branching involved in prostate gland morphogenesis / intra-Golgi vesicle-mediated transport / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / Cul2-RING ubiquitin ligase complex ...regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / Intra-Golgi traffic / branching involved in prostate gland morphogenesis / intra-Golgi vesicle-mediated transport / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / Golgi membrane / apoptotic process / Golgi apparatus / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Chen, X. / Zhang, K. / Xu, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of Ψ-Pro/C-degron recognition by the CRL2 ubiquitin ligase. Authors: Xinyan Chen / Anat Raiff / Shanshan Li / Qiong Guo / Jiahai Zhang / Hualin Zhou / Richard T Timms / Xuebiao Yao / Stephen J Elledge / Itay Koren / Kaiming Zhang / Chao Xu / ![]() ![]() ![]() ![]() Abstract: The E3 ligase-degron interaction determines the specificity of the ubiquitin‒proteasome system. We recently discovered that FEM1B, a substrate receptor of Cullin 2-RING ligase (CRL2), recognizes C- ...The E3 ligase-degron interaction determines the specificity of the ubiquitin‒proteasome system. We recently discovered that FEM1B, a substrate receptor of Cullin 2-RING ligase (CRL2), recognizes C-degrons containing a C-terminal proline. By solving several cryo-EM structures of CRL2 bound to different C-degrons, we elucidate the dimeric assembly of the complex. Furthermore, we reveal distinct dimerization states of unmodified and neddylated CRL2 to uncover the NEDD8-mediated activation mechanism of CRL2. Our research also indicates that, FEM1B utilizes a bipartite mechanism to recognize both the C-terminal proline and an upstream aromatic residue within the substrate. These structural findings, complemented by in vitro ubiquitination and in vivo cell-based assays, demonstrate that CRL2-mediated polyubiquitination and subsequent protein turnover depend on both FEM1B-degron interactions and the dimerization state of the E3 ligase complex. Overall, this study deepens our molecular understanding of how Cullin-RING E3 ligase substrate selection mediates protein turnover. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.1 KB | Display | ![]() |
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PDB format | ![]() | 102.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 37746MC ![]() 8wqaC ![]() 8wqbC ![]() 8wqcC ![]() 8wqdC ![]() 8wqeC ![]() 8wqfC ![]() 8wqgC ![]() 8wqhC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 70355.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3143.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Local refinement of FEM1B bound with the C-degron of CUX1 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 1500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 57.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 8112 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 206765 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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