7B5L

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1

Summary for 7B5L

• Entry DOI: 10.2210/pdb7b5l/pdb
• EMDB information: 12004 12005 12006 12007 12037
• Descriptor: Cullin-1, Cyclin-dependent kinase 2, Cyclin-A2, ... (14 entities in total)
• Functional Keywords: ubiquitin, ubiquitin ligase, e3 ligase, f-box protein, rbr ligase, cullin-ring-ligase, crl, scf, nedd8, post-translational modification, ubiquitylation, ligase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 12
• Total formula weight: 382217.52

Authors

Horn-Ghetko, D.,Prabu, J.R.,Schulman, B.A. (deposition date: 2020-12-04, release date: 2021-02-10, Last modification date: 2024-10-23)

Primary citation

Horn-Ghetko, D.,Krist, D.T.,Prabu, J.R.,Baek, K.,Mulder, M.P.C.,Klugel, M.,Scott, D.C.,Ovaa, H.,Kleiger, G.,Schulman, B.A.
Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly.
Nature, 590:671-676, 2021

PubMed Abstract: E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates. However, rather than functioning individually, many neddylated cullin-RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family-which together account for nearly half of all ubiquitin ligases in humans-form E3-E3 super-assemblies. Here, by studying CRLs in the SKP1-CUL1-F-box (SCF) family, we show how neddylated SCF ligases and ARIH1 (an RBR-type E3 ligase) co-evolved to ubiquitylate diverse substrates presented on various F-box proteins. We developed activity-based chemical probes that enabled cryo-electron microscopy visualization of steps in E3-E3 ubiquitylation, initiating with ubiquitin linked to the E2 enzyme UBE2L3, then transferred to the catalytic cysteine of ARIH1, and culminating in ubiquitin linkage to a substrate bound to the SCF E3 ligase. The E3-E3 mechanism places the ubiquitin-linked active site of ARIH1 adjacent to substrates bound to F-box proteins (for example, substrates with folded structures or limited length) that are incompatible with previously described conventional RING E3-only mechanisms. The versatile E3-E3 super-assembly may therefore underlie widespread ubiquitylation.

PubMed: 33536622
DOI: 10.1038/s41586-021-03197-9

Experimental method

ELECTRON MICROSCOPY (3.8 Å)