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TitleATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 4414, Year 2025
Publish dateMay 13, 2025
AuthorsJuraj Ahel / Arda Balci / Victoria Faas / Daniel B Grabarczyk / Roosa Harmo / Daniel R Squair / Jiazhen Zhang / Elisabeth Roitinger / Frederic Lamoliatte / Sunil Mathur / Luiza Deszcz / Lillie E Bell / Anita Lehner / Thomas L Williams / Hanna Sowar / Anton Meinhart / Nicola T Wood / Tim Clausen / Satpal Virdee / Adam J Fletcher /
PubMed AbstractThe 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 ...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.
External linksNat Commun / PubMed:40360510 / PubMed Central
MethodsEM (single particle)
Resolution3.8 - 4.5 Å
Structure data

52570

9i1i

EMDB-52570, PDB-9i1i:
Cryo-EM structure of mouse RNF213 (WB3/WB4 + ATP)
Method: EM (single particle) / Resolution: 4.5 Å

52571

9i1j

EMDB-52571, PDB-9i1j:
Cryo-EM structure of mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized, and ATPgS
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • mus musculus (house mouse)
  • homo sapiens (human)
KeywordsLIGASE / E3 ligase / ubiquitin / AAA ATPase

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