8T9A

CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3

Summary for 8T9A

• Entry DOI: 10.2210/pdb8t9a/pdb
• EMDB information: 41105
• Descriptor: DNA damage-binding protein 1, DDB1- and CUL4-associated factor 12, Melanoma-associated antigen 3 (3 entities in total)
• Functional Keywords: dcaf12, dna damage-binding protein 1, ddb1, e3 ligase, ligase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 203890.74

Authors

Duda, D.,Righetto, G.,Li, Y.,Loppnau, P.,Seitova, A.,Santhakumar, V.,Halabelian, L.,Yin, Y. (deposition date: 2023-06-23, release date: 2024-04-10, Last modification date: 2025-05-21)

Primary citation

Righetto, G.L.,Yin, Y.,Duda, D.M.,Vu, V.,Szewczyk, M.M.,Zeng, H.,Li, Y.,Loppnau, P.,Mei, T.,Li, Y.Y.,Seitova, A.,Patrick, A.N.,Brazeau, J.F.,Chaudhry, C.,Barsyte-Lovejoy, D.,Santhakumar, V.,Halabelian, L.
Probing the CRL4 DCAF12 interactions with MAGEA3 and CCT5 di-Glu C-terminal degrons.
Pnas Nexus, 3:pgae153-pgae153, 2024

PubMed Abstract: Damaged DNA-binding protein-1 (DDB1)- and CUL4-associated factor 12 (DCAF12) serves as the substrate recognition component within the Cullin4-RING E3 ligase (CRL4) complex, capable of identifying C-terminal double-glutamic acid degrons to promote the degradation of specific substrates through the ubiquitin proteasome system. Melanoma-associated antigen 3 (MAGEA3) and T-complex protein 1 subunit epsilon (CCT5) proteins have been identified as cellular targets of DCAF12. To further characterize the interactions between DCAF12 and both MAGEA3 and CCT5, we developed a suite of biophysical and proximity-based cellular NanoBRET assays showing that the C-terminal degron peptides of both MAGEA3 and CCT5 form nanomolar affinity interactions with DCAF12 in vitro and in cells. Furthermore, we report here the 3.17 Å cryo-EM structure of DDB1-DCAF12-MAGEA3 complex revealing the key DCAF12 residues responsible for C-terminal degron recognition and binding. Our study provides new insights and tools to enable the discovery of small molecule handles targeting the WD40-repeat domain of DCAF12 for future proteolysis targeting chimera design and development.

PubMed: 38665159
DOI: 10.1093/pnasnexus/pgae153

Experimental method

ELECTRON MICROSCOPY (3.17 Å)