9NR3 | pdb_00009nr3

CRBN-DDB1 in complex with GLUL-cN

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2025-03-13 Released: 2026-01-07 
  • Deposition Author(s): Cao, S., Zheng, N.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 
    0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

PCMT1 generates the C-terminal cyclic imide degron on CRBN substrates.

Zhao, Z.Xu, W.Feng, E.Y.Cao, S.Hermoso-Lopez, A.Pena-Vega, P.Lloyd, H.C.Porter, A.K.D.Guzman, M.Zheng, N.Woo, C.M.

(2025) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-025-02106-9
  • Primary Citation of Related Structures:  
    9NR3

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1826Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon402Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
GTEx:  ENSG00000113851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GLUL-cNC [auth D]6Homo sapiensMutation(s): 0 
EC: 2.3.1.225 (UniProt), 6.3.1.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15104 (Homo sapiens)
Explore P15104 
Go to UniProtKB:  P15104
PHAROS:  P15104
GTEx:  ENSG00000135821 
Entity Groups  
UniProt GroupP15104
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SNN
Query on SNN
C [auth D]L-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.435α = 90
b = 100.364β = 90
c = 169.672γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-07
    Type: Initial release