6H0G

Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.25 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN.

Sievers, Q.L., Petzold, G., Bunker, R.D., Renneville, A., Slabicki, M., Liddicoat, B.J., Abdulrahman, W., Mikkelsen, T., Ebert, B.L., Thoma, N.H.

(2018) Science 362

  • DOI: https://doi.org/10.1126/science.aat0572
  • Primary Citation of Related Structures:  
    6H0F, 6H0G

  • PubMed Abstract: 

    • The small molecules thalidomide, lenalidomide, and pomalidomide induce the ubiquitination and proteasomal degradation of the transcription factors Ikaros (IKZF1) and Aiolos (IKZF3) by recruiting a Cys 2 -His 2 (C2H2) zinc finger domain to Cereblon (CRBN), the substrate receptor of the CRL4 CRBN E3 ubiquitin ligase ...

    The small molecules thalidomide, lenalidomide, and pomalidomide induce the ubiquitination and proteasomal degradation of the transcription factors Ikaros (IKZF1) and Aiolos (IKZF3) by recruiting a Cys 2 -His 2 (C2H2) zinc finger domain to Cereblon (CRBN), the substrate receptor of the CRL4 CRBN E3 ubiquitin ligase. We screened the human C2H2 zinc finger proteome for degradation in the presence of thalidomide analogs, identifying 11 zinc finger degrons. Structural and functional characterization of the C2H2 zinc finger degrons demonstrates how diverse zinc finger domains bind the permissive drug-CRBN interface. Computational zinc finger docking and biochemical analysis predict that more than 150 zinc fingers bind the drug-CRBN complex in vitro, and we show that selective zinc finger degradation can be achieved through compound modifications. Our results provide a rationale for therapeutically targeting transcription factors that were previously considered undruggable.

    Organizational Affiliation: 

    Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland. benajmin_ebert@dfci.harvard.edu nicolas.thoma@fmi.ch.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DDB1 (DNA damage binding protein 1),DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
A, D
856Homo sapiensMutation(s): 0 
Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
Entity Groups  
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UniProt GroupQ16531
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein cereblon
B, E
426Homo sapiensMutation(s): 0 
Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
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UniProt GroupQ96SW2
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein 692
C, F
31Homo sapiensMutation(s): 0 
Gene Names: ZNF692, AREBP, ZFP692
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BU19 (Homo sapiens)
Explore Q9BU19 
Go to UniProtKB:  Q9BU19
PHAROS:  Q9BU19
Entity Groups  
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UniProt GroupQ9BU19
Protein Feature View
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Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
Y70 BindingDB:  6H0G Ki: 1.00e+4 (nM) from 1 assay(s)
IC50: min: 63.1, max: 2.58e+4 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.25 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.51α = 90
b = 99.53β = 108.49
c = 166.94γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European UnionHorizon 2020 No. 666068
European Molecular Biology OrganizationAdvanced Fellowship aALTF 761-2016
European UnionHuman Frontier Science Program Long-Term Fellowship LT000210/2014

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 2.0: 2019-04-17
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary