9I1J

Cryo-EM structure of mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized, and ATPgS

9I1J の概要

• エントリーDOI: 10.2210/pdb9i1j/pdb
• EMDBエントリー: 52571
• 分子名称: E3 ubiquitin-protein ligase RNF213, Ubiquitin-conjugating enzyme E2 L3, ADENOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• 機能のキーワード: e3 ligase, ubiquitin, aaa atpase, ligase
• 由来する生物種: Mus musculus (house mouse); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 573337.99

構造登録者

Grabarczyk, D.B.,Ahel, J.,Clausen, T. (登録日: 2025-01-16, 公開日: 2025-12-10)

主引用文献

Ahel, J.,Balci, A.,Faas, V.,Grabarczyk, D.B.,Harmo, R.,Squair, D.R.,Zhang, J.,Roitinger, E.,Lamoliatte, F.,Mathur, S.,Deszcz, L.,Bell, L.E.,Lehner, A.,Williams, T.L.,Sowar, H.,Meinhart, A.,Wood, N.T.,Clausen, T.,Virdee, S.,Fletcher, A.J.
ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213.
Nat Commun, 16:4414-4414, 2025

PubMed Abstract: The giant E3 ubiquitin ligase RNF213 is a conserved component of mammalian cell-autonomous immunity, limiting the replication of bacteria, viruses and parasites. To understand how RNF213 reacts to these unrelated pathogens, we employ chemical and structural biology to find that ATP binding to its ATPases Associated with diverse cellular Activities (AAA) core activates its E3 function. We develop methodology for proteome-wide E3 activity profiling inside living cells, revealing that RNF213 undergoes a reversible switch in E3 activity in response to cellular ATP abundance. Interferon stimulation of macrophages raises intracellular ATP levels and primes RNF213 E3 activity, while glycolysis inhibition depletes ATP and downregulates E3 activity. These data imply that ATP bears hallmarks of a danger/pathogen associated molecular pattern, coordinating cell-autonomous defence. Furthermore, quantitative labelling of RNF213 with E3-activity probes enabled us to identify the catalytic cysteine required for substrate ubiquitination and obtain a cryo-EM structure of the RNF213-E2-ubiquitin conjugation enzyme transfer intermediate, illuminating an unannotated E2 docking site. Together, our data demonstrate that RNF213 represents a new class of ATP-dependent E3 enzyme, employing distinct catalytic and regulatory mechanisms adapted to its specialised role in the broad defence against intracellular pathogens.

PubMed: 40360510
DOI: 10.1038/s41467-025-59444-4

実験手法

ELECTRON MICROSCOPY (3.8 Å)