8Q7R

Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting.

Li, J.Purser, N.Liwocha, J.Scott, D.C.Byers, H.A.Steigenberger, B.Hill, S.Tripathi-Giesgen, I.Hinkle, T.Hansen, F.M.Prabu, J.R.Radhakrishnan, S.K.Kirkpatrick, D.S.Reichermeier, K.M.Schulman, B.A.Kleiger, G.

(2024) Mol Cell 84: 1304

  • DOI: https://doi.org/10.1016/j.molcel.2024.01.022
  • Primary Citation of Related Structures:  
    8Q7R, 8R5H

  • PubMed Abstract: 

    Cullin-RING ligases (CRLs) ubiquitylate specific substrates selected from other cellular proteins. Substrate discrimination and ubiquitin transferase activity were thought to be strictly separated. Substrates are recognized by substrate receptors, such as Fbox or BCbox proteins. Meanwhile, CRLs employ assorted ubiquitin-carrying enzymes (UCEs, which are a collection of E2 and ARIH-family E3s) specialized for either initial substrate ubiquitylation (priming) or forging poly-ubiquitin chains. We discovered specific human CRL-UCE pairings governing substrate priming. The results reveal pairing of CUL2-based CRLs and UBE2R-family UCEs in cells, essential for efficient PROTAC-induced neo-substrate degradation. Despite UBE2R2's intrinsic programming to catalyze poly-ubiquitylation, CUL2 employs this UCE for geometrically precise PROTAC-dependent ubiquitylation of a neo-substrate and for rapid priming of substrates recruited to diverse receptors. Cryo-EM structures illuminate how CUL2-based CRLs engage UBE2R2 to activate substrate ubiquitylation. Thus, pairing with a specific UCE overcomes E2 catalytic limitations to drive substrate ubiquitylation and targeted protein degradation.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-2745Homo sapiensMutation(s): 0 
Gene Names: CUL2
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PHAROS:  Q13617
GTEx:  ENSG00000108094 
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UniProt GroupQ13617
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein fem-1 homolog CB [auth H]617Homo sapiensMutation(s): 0 
Gene Names: FEM1CKIAA1785
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GTEx:  ENSG00000145780 
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UniProt GroupQ96JP0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinC [auth U]685Homo sapiensMutation(s): 0 
Gene Names: UBC
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PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleotide exchange factor SIL1D [auth F]20Homo sapiensMutation(s): 7 
Gene Names: SIL1UNQ545/PRO836
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 R2E [auth C]238Homo sapiensMutation(s): 0 
Gene Names: UBE2R2CDC34BUBC3B
EC: 2.3.2.23
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CF [auth D]112Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1H [auth R]108Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references
  • Version 1.2: 2024-04-17
    Changes: Derived calculations
  • Version 1.3: 2024-04-24
    Changes: Database references
  • Version 1.4: 2024-10-23
    Changes: Data collection, Structure summary