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TitleMolecular basis of SIFI activity in the integrated stress response.
Journal, issue, pagesNature, Year 2025
Publish dateMay 6, 2025
AuthorsZhi Yang / Diane L Haakonsen / Michael Heider / Samuel R Witus / Alex Zelter / Tobias Beschauner / Michael J MacCoss / Michael Rapé /
PubMed AbstractChronic stress response activation impairs cell survival and causes devastating degenerative diseases. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor ...Chronic stress response activation impairs cell survival and causes devastating degenerative diseases. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor of the integrated stress response (SIFI), to terminate stress response signalling and ensure cellular homeostasis. How a silencing factor can sense stress across cellular scales to elicit timely stress response inactivation is poorly understood. Here we combine cryo-electron microscopy analysis of endogenous SIFI with AlphaFold modelling and biochemical studies to report the structural and mechanistic basis of the silencing of the integrated stress response. SIFI detects both stress indicators and stress response components through flexible domains within an easily accessible scaffold, before building linkage-specific ubiquitin chains at separate, sterically restricted elongation modules. Ubiquitin handover by a ubiquitin-like domain couples versatile substrate modification to linkage-specific ubiquitin polymer formation. Stress response silencing therefore exploits a catalytic mechanism that is geared towards processing many diverse proteins and therefore allows a single enzyme to monitor and, if needed, modulate a complex cellular state.
External linksNature / PubMed:40328314
MethodsEM (single particle)
Resolution3.1 - 3.4 Å
Structure data

46686

9d9z

EMDB-46686, PDB-9d9z:
Structure of human UBR4-KCMF1-CaM E3 ligase complex (Silencing Factor of the Integrated stress response, SiFI)
Method: EM (single particle) / Resolution: 3.4 Å

46688

9nwd

EMDB-46688: Cryo-EM map of the human UBR4-KCMF1-CaM E3 Ligase complex (Silencing Factor of the Integrated stress response, SiFI) N-terminal region
PDB-9nwd: Human E3 ligase UBR4-KCMF1-calmodulin complex (N-terminal)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-46742: Structure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A)
Method: EM (single particle) / Resolution: 3.1 Å

49876

9nwe

EMDB-49876, PDB-9nwe:
E3 ligase UBR4-KCMF1-calmodulin complex
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

Source
  • homo sapiens (human)
KeywordsLIGASE / E3 liase / UBR4 / SIFI / E3 ligase / ISR

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