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Crystal structure of the SALL4–pomalidomide–cereblon–DDB1 complex


Thalidomide-dependent degradation of the embryonic transcription factor SALL4 by the CRL4CRBN E3 ubiquitin ligase is a plausible major driver of thalidomide teratogenicity. The structure of the second zinc finger of SALL4 in complex with pomalidomide, cereblon and DDB1 reveals the molecular details of recruitment. Sequence differences and a shifted binding position relative to Ikaros offer a path to the rational design of cereblon-binding drugs with reduced teratogenic risk.

Fig. 1: Structure of cereblon in complex with DDB1, pomalidomide and SALL4 ZF2.
Fig. 2: Effect of H417 on SALL4 binding mode.

Data availability

All data generated or analyzed during this study are included in this manuscript with the exception of structure coordinates and structure factors, which have been deposited into the Protein Data Bank under accession code 6UML. Source data for Fig. 2 are presented with the paper.


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Thanks to M. Riley for baculovirus expression support and J. Pack, M. Ellis and L. LeBrun for thoughtful comments on the manuscript. This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357.

Author information




T.C., E.T., B.P., A.C., M.E.M. and P.P.C. performed crystallographic studies and in vitro assays. X.Z. and G.L. performed immunoprecipitation experiments. C.M. and J.M. performed molecular dynamics simulations. M.R., L.G.H. and P.P.C. planned the research.

Corresponding authors

Correspondence to Mary E. Matyskiela or Philip P. Chamberlain.

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Competing interests

The authors are, or have been, employees or contractors of Celgene and/or Bristol-Myers Squibb.

Additional information

Peer review information Katarzyna Marcinkiewicz was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Sample electron density from the cereblon-DDB1-SALL4 ZF2-pomalidomide crystal structure.

Fo-Fc electron density map calculated in the absence of pomalidomide and contoured at 3σ following a round of refinement. Protein atoms are not shown in the figure.

Extended Data Fig. 2 SALL4 binding defects upon cereblon mutation mapped onto the structure of cereblon.

The surface of cereblon is colored by the effect of alanine mutations at that position on SALL4 ternary complex formation (blue, untested; green, no effect; red, detrimental effect; magenta, increased complex formation).

Extended Data Fig. 3 Structural model of SALL4 recruitment by the CRL4CRBN complex.

Structural model of SALL4 recruitment by pomalidomide to the cereblon-CRL4 E3 ligase complex, positioning SALL4 nearby the site of E2 recruitment on RBX11.

Supplementary information

Source data

Source Data Fig. 2

Unprocessed western blots.

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Matyskiela, M.E., Clayton, T., Zheng, X. et al. Crystal structure of the SALL4–pomalidomide–cereblon–DDB1 complex. Nat Struct Mol Biol 27, 319–322 (2020).

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