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- PDB-8wqi: Local refinement of FEM1B bound with the C-degron of CUX1 -

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Basic information

Entry
Database: PDB / ID: 8wqi
TitleLocal refinement of FEM1B bound with the C-degron of CUX1
Components
  • Protein CASP
  • Protein fem-1 homolog B
KeywordsPROTEIN BINDING / E3 ubiquitin ligase / Pro/C-degron
Function / homology
Function and homology information


regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / Intra-Golgi traffic / branching involved in prostate gland morphogenesis / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / intra-Golgi vesicle-mediated transport / regulation of extrinsic apoptotic signaling pathway via death domain receptors / death receptor binding / 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 / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / intra-Golgi vesicle-mediated transport / regulation of extrinsic apoptotic signaling pathway via death domain receptors / death receptor binding / Cul2-RING ubiquitin ligase complex / 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 / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
CASP, C-terminal / CASP C terminal / CUX1-like, N-terminal tRNA-binding arm / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Protein CASP / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen, X. / Zhang, K. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
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
DepositionOct 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Protein fem-1 homolog B
G: Protein CASP


Theoretical massNumber of molelcules
Total (without water)73,4982
Polymers73,4982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein fem-1 homolog B / FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic ...FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic pathway protein alpha / F1A-alpha


Mass: 70355.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1B, F1AA, KIAA0396 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UK73
#2: Protein/peptide Protein CASP


Mass: 3143.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUX1, CUTL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13948

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Local refinement of FEM1B bound with the C-degron of CUX1
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 57.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 8112
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2cryoSPARCimage acquisition
9PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 206765 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035165
ELECTRON MICROSCOPYf_angle_d0.6026999
ELECTRON MICROSCOPYf_dihedral_angle_d4.605700
ELECTRON MICROSCOPYf_chiral_restr0.04803
ELECTRON MICROSCOPYf_plane_restr0.005909

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