9OMF

Cryo-EM structure of neddylated PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5-PCMTD1)

Summary for 9OMF

• Entry DOI: 10.2210/pdb9omf/pdb
• Related: 9OMA
• EMDB information: 70612
• Descriptor: Protein-L-isoaspartate O-methyltransferase domain-containing protein 1, Cullin-5, RING-box protein 2, ... (5 entities in total)
• Functional Keywords: cul5-ring ubiquitin ligase complex, protein binding
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 168963.73

Authors

Pang, E.Z.,Zhao, B.,Flowers, C.,Oroudjeva, E.,Winters, J.B.,Pandey, V.,Sawaya, M.R.,Wohlschlegel, W.,Loo, J.A.,Rodriguez, J.A.,Clarke, S.G. (deposition date: 2025-05-13, release date: 2025-06-04, Last modification date: 2025-06-18)

Primary citation

Pang, E.Z.,Zhao, B.,Flowers, C.,Oroudjeva, E.,Winter, J.B.,Pandey, V.,Sawaya, M.R.,Wohlschlegel, J.,Loo, J.A.,Rodriguez, J.A.,Clarke, S.G.
Structural basis for L-isoaspartyl-containing protein recognition by the PCMTD1 cullin-RING E3 ubiquitin ligase.
Biorxiv, 2025

PubMed Abstract: A major type of spontaneous protein damage that accumulates with age is the formation of kinked polypeptide chains with L-isoaspartyl residues. Mitigating this damage is necessary for maintaining proteome stability and prolonging organismal survival. While repair through methylation by PCMT1 has been previously shown to suppress L-isoaspartyl accumulation, we provide an additional mechanism for L-isoaspartyl maintenance through PCMTD1, a cullin-RING ligase (CRL). We combined cryo-EM, native mass spectrometry, and biochemical assays to provide insight on how the assembly and architecture of PCMTD1 in the context of a CRL complex fulfils this alternative mechanism. We show that the PCMTD1 CRL complex specifically binds L-isoaspartyl residues when bound to AdoMet. This work provides evidence for a growing class of E3 ubiquitin ligases that recognize spontaneous covalent modifications as potential substrates for ubiquitylation and subsequent proteasomal degradation.

PubMed: 40475564
DOI: 10.1101/2025.05.21.654933

Experimental method

ELECTRON MICROSCOPY (9.72 Å)