9NR3 image
Deposition Date 2025-03-13
Release Date 2026-01-07
Last Version Date 2026-01-07
Entry Detail
PDB ID:
9NR3
Keywords:
Title:
CRBN-DDB1 in complex with GLUL-cN
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.93 Å
R-Value Free:
0.27
R-Value Work:
0.24
R-Value Observed:
0.25
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA damage-binding protein 1
Gene (Uniprot):DDB1
Chain IDs:A
Chain Length:826
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein cereblon
Gene (Uniprot):CRBN
Chain IDs:B
Chain Length:402
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GLUL-cN
Gene (Uniprot):GLUL
Chain IDs:C (auth: D)
Chain Length:6
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SNN C ASN modified residue
Ligand Molecules
Primary Citation
PCMT1 generates the C-terminal cyclic imide degron on CRBN substrates.
Nat.Chem.Biol. ? ? ? (2025)
PMID: 41461925 DOI: 10.1038/s41589-025-02106-9

Abstact

The E3 ligase substrate adapter cereblon (CRBN), the primary target of clinical agents thalidomide and lenalidomide, recognizes endogenous substrates bearing the C-terminal cyclic imide modification. Although C-terminal cyclic imides can form spontaneously, an enzyme that regulates their formation and thereby promotes a biological pathway connecting substrates to CRBN is unknown. Here we report that protein carboxymethyltransferase (PCMT1) promotes formation of C-terminal cyclic imides on C-terminal asparagine residues of CRBN substrates. PCMT1 and CRBN coregulate the levels of metabolic enzymes including glutamine synthetase and inorganic pyrophosphatase 1 in vitro, in cells and in vivo, and this regulation is associated with the proepileptic phenotype of CRBN knockout mouse models. The discovery of an enzyme that regulates CRBN substrates through the C-terminal cyclic imide reveals a previously unknown biological pathway that is perturbed by thalidomide derivatives and provides a biochemical basis for the connection between multiple biological processes and CRBN.

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Chemical

Disease

Primary Citation of related structures
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