7OKQ

Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex

Summary for 7OKQ

• Entry DOI: 10.2210/pdb7okq/pdb
• EMDB information: 12964
• Descriptor: DNA damage-binding protein 1, DDB1- and CUL4-associated factor 1, Cullin-4A, ... (4 entities in total)
• Functional Keywords: ubiquitin, e3, protein degradation, ligase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 16
• Total formula weight: 1603496.27

Authors

Mohamed, W.I.,Schenk, A.D.,Kempf, G.,Cavadini, S.,Thoma, N.H. (deposition date: 2021-05-18, release date: 2021-10-13, Last modification date: 2024-07-10)

Primary citation

Mohamed, W.I.,Schenk, A.D.,Kempf, G.,Cavadini, S.,Basters, A.,Potenza, A.,Abdul Rahman, W.,Rabl, J.,Reichermeier, K.,Thoma, N.H.
The CRL4 DCAF1 cullin-RING ubiquitin ligase is activated following a switch in oligomerization state.
Embo J., 40:e108008-e108008, 2021

PubMed Abstract: The cullin-4-based RING-type (CRL4) family of E3 ubiquitin ligases functions together with dedicated substrate receptors. Out of the ˜29 CRL4 substrate receptors reported, the DDB1- and CUL4-associated factor 1 (DCAF1) is essential for cellular survival and growth, and its deregulation has been implicated in tumorigenesis. We carried out biochemical and structural studies to examine the structure and mechanism of the CRL4 ligase. In the 8.4 Å cryo-EM map of CRL4 , four CUL4-RBX1-DDB1-DCAF1 protomers are organized into two dimeric sub-assemblies. In this arrangement, the WD40 domain of DCAF1 mediates binding with the cullin C-terminal domain (CTD) and the RBX1 subunit of a neighboring CRL4 protomer. This renders RBX1, the catalytic subunit of the ligase, inaccessible to the E2 ubiquitin-conjugating enzymes. Upon CRL4 activation by neddylation, the interaction between the cullin CTD and the neighboring DCAF1 protomer is broken, and the complex assumes an active dimeric conformation. Accordingly, a tetramerization-deficient CRL4 mutant has higher ubiquitin ligase activity compared to the wild-type. This study identifies a novel mechanism by which unneddylated and substrate-free CUL4 ligases can be maintained in an inactive state.

PubMed: 34595758
DOI: 10.15252/embj.2021108008

Experimental method

ELECTRON MICROSCOPY (8.4 Å)