4CI3

Structure of the DDB1-CRBN E3 ubiquitin ligase bound to Pomalidomide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Ddb1-Crbn E3 Ubiquitin Ligase in Complex with Thalidomide.

Fischer, E.S.Bohm, K.Lydeard, J.R.Yang, H.Stadler, M.B.Cavadini, S.Nagel, J.Serluca, F.Acker, V.Lingaraju, G.M.Tichkule, R.B.Schebesta, M.Forrester, W.C.Schirle, M.Hassiepen, U.Ottl, J.Hild, M.Beckwith, R.E.J.Harper, J.W.Jenkins, J.L.Thoma, N.H.

(2014) Nature 512: 49

  • DOI: 10.1038/nature13527
  • Primary Citation of Related Structures:  
    4CI2, 4CI3, 4CI1

  • PubMed Abstract: 
  • In the 1950s, the drug thalidomide, administered as a sedative to pregnant women, led to the birth of thousands of children with multiple defects. Despite the teratogenicity of thalidomide and its derivatives lenalidomide and pomalidomide, these immu ...

    In the 1950s, the drug thalidomide, administered as a sedative to pregnant women, led to the birth of thousands of children with multiple defects. Despite the teratogenicity of thalidomide and its derivatives lenalidomide and pomalidomide, these immunomodulatory drugs (IMiDs) recently emerged as effective treatments for multiple myeloma and 5q-deletion-associated dysplasia. IMiDs target the E3 ubiquitin ligase CUL4-RBX1-DDB1-CRBN (known as CRL4(CRBN)) and promote the ubiquitination of the IKAROS family transcription factors IKZF1 and IKZF3 by CRL4(CRBN). Here we present crystal structures of the DDB1-CRBN complex bound to thalidomide, lenalidomide and pomalidomide. The structure establishes that CRBN is a substrate receptor within CRL4(CRBN) and enantioselectively binds IMiDs. Using an unbiased screen, we identified the homeobox transcription factor MEIS2 as an endogenous substrate of CRL4(CRBN). Our studies suggest that IMiDs block endogenous substrates (MEIS2) from binding to CRL4(CRBN) while the ligase complex is recruiting IKZF1 or IKZF3 for degradation. This dual activity implies that small molecules can modulate an E3 ubiquitin ligase and thereby upregulate or downregulate the ubiquitination of proteins.


    Organizational Affiliation

    1] Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland [2] University of Basel, Petersplatz 10, CH-4003 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA DAMAGE-BINDING PROTEIN 1A1158Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
NIH Common Fund Data Resources
PHAROS  Q16531
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN CEREBLONB469Gallus gallusMutation(s): 0 
Gene Names: CRBN
Find proteins for P0CF65 (Gallus gallus)
Explore P0CF65 
Go to UniProtKB:  P0CF65
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y70
Query on Y70

Download CCD File 
B
S-Pomalidomide
C13 H11 N3 O4
UVSMNLNDYGZFPF-QMMMGPOBSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y70IC50:  1200   nM  BindingDB
Y70IC50:  3000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.07α = 90
b = 171.07β = 90
c = 137.93γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-08-13
    Changes: Database references
  • Version 1.3: 2019-03-27
    Changes: Data collection, Other, Source and taxonomy