8PQL

K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases.

Liwocha, J.Li, J.Purser, N.Rattanasopa, C.Maiwald, S.Krist, D.T.Scott, D.C.Steigenberger, B.Prabu, J.R.Schulman, B.A.Kleiger, G.

(2024) Nat Struct Mol Biol 31: 378-389

  • DOI: https://doi.org/10.1038/s41594-023-01206-1
  • Primary Citation of Related Structures:  
    8PQL

  • PubMed Abstract: 

    E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked poly-ubiquitin chains to control an enormous swath of eukaryotic biology. Yet the molecular mechanisms underlying this exceptional linkage specificity and millisecond kinetics of poly-ubiquitylation remain unclear. Here we obtain cryogenic-electron microscopy (cryo-EM) structures that provide pertinent insight into how such poly-ubiquitin chains are forged. The CRL RING domain not only activates the E2-bound ubiquitin but also shapes the conformation of a distinctive UBE2R2 loop, positioning both the ubiquitin to be transferred and the substrate-linked acceptor ubiquitin within the active site. The structures also reveal how the ubiquitin-like protein NEDD8 uniquely activates CRLs during chain formation. NEDD8 releases the RING domain from the CRL, but unlike previous CRL-E2 structures, does not contact UBE2R2. These findings suggest how poly-ubiquitylation may be accomplished by many E2s and E3s.


  • Organizational Affiliation

    Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 R2A [auth C]238Homo sapiensMutation(s): 0 
Gene Names: UBE2R2CDC34BUBC3B
EC: 2.3.2.23
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Find proteins for Q712K3 (Homo sapiens)
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PHAROS:  Q712K3
GTEx:  ENSG00000107341 
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UniProt GroupQ712K3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-C,Nucleotide exchange factor SIL1B [auth E]704Homo sapiensMutation(s): 7 
Gene Names: UBCSIL1UNQ545/PRO836
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PHAROS:  Q9H173
GTEx:  ENSG00000120725 
Find proteins for P0CG48 (Homo sapiens)
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PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupsQ9H173P0CG48
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein fem-1 homolog CC [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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1D [auth K]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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GTEx:  ENSG00000100387 
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UniProt GroupP62877
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinE [auth U]685Homo sapiensMutation(s): 1 
Gene Names: UBC
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PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-2F [auth A]745Homo sapiensMutation(s): 0 
Gene Names: CUL2
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GTEx:  ENSG00000108094 
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UniProt GroupQ13617
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CG [auth D]112Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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Find proteins for Q15369 (Homo sapiens)
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GTEx:  ENSG00000154582 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-BH [auth G]118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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Find proteins for Q15370 (Homo sapiens)
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GTEx:  ENSG00000103363 
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UniProt GroupQ15370
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.76 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: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Database references
  • Version 1.3: 2024-04-17
    Changes: Derived calculations, Structure summary