7OKQ image
Deposition Date 2021-05-18
Release Date 2021-10-13
Last Version Date 2024-07-10
Entry Detail
PDB ID:
7OKQ
Keywords:
Title:
Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
8.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA damage-binding protein 1
Gene (Uniprot):DDB1
Chain IDs:A, E, I, M
Chain Length:1159
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:DDB1- and CUL4-associated factor 1
Gene (Uniprot):DCAF1
Chain IDs:B, F, J, N
Chain Length:1525
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Cullin-4A
Gene (Uniprot):CUL4A
Chain IDs:C, G, K, O
Chain Length:742
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase RBX1
Gene (Uniprot):RBX1
Chain IDs:D, H, L, P
Chain Length:116
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
The CRL4 DCAF1 cullin-RING ubiquitin ligase is activated following a switch in oligomerization state.
Embo J. 40 e108008 e108008 (2021)
PMID: 34595758 DOI: 10.15252/embj.2021108008

Abstact

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 CRL4DCAF1 ligase. In the 8.4 Å cryo-EM map of CRL4DCAF1 , 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 CRL4DCAF1 protomer. This renders RBX1, the catalytic subunit of the ligase, inaccessible to the E2 ubiquitin-conjugating enzymes. Upon CRL4DCAF1 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 CRL4DCAF1 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.

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Primary Citation of related structures