Autoinhibition of dimeric NINJ1 prevents plasma membrane rupture

Sergei Pourmal, Melissa E. Truong, Matthew C. Johnson, Ying Yang, Lijuan Zhou, Kamela Alegre, Irma B. Stowe, Shalini Gupta, Phoebe A. Chen, Yingnan Zhang, Alexis Rohou, Kim Newton, Nobuhiko Kayagaki, Vishva M. Dixit () and Ishan Deshpande ()
Additional contact information
Sergei Pourmal: Genentech
Melissa E. Truong: Genentech
Matthew C. Johnson: Genentech
Ying Yang: Genentech
Lijuan Zhou: Genentech
Kamela Alegre: Genentech
Irma B. Stowe: Genentech
Shalini Gupta: Genentech
Phoebe A. Chen: Genentech
Yingnan Zhang: Genentech
Alexis Rohou: Genentech
Kim Newton: Genentech
Nobuhiko Kayagaki: Genentech
Vishva M. Dixit: Genentech
Ishan Deshpande: Genentech

Nature, 2025, vol. 637, issue 8045, 446-452

Abstract: Abstract Lytic cell death culminates in plasma membrane rupture, which releases large intracellular molecules to augment the inflammatory response. Plasma membrane rupture is mediated by the effector membrane protein ninjurin-1 (NINJ1)1, which polymerizes and ruptures the membrane via its hydrophilic face1–4. How NINJ1 is restrained under steady-state conditions to ensure cell survival remains unknown. Here we describe the molecular underpinnings of NINJ1 inhibition. Using cryogenic electron microscopy, we determined the structure of inactive-state mouse NINJ1 bound to the newly developed nanobody Nb538. Inactive NINJ1 forms a face-to-face homodimer by adopting a three-helix conformation with unkinked transmembrane helix 1 (TM1), in contrast to the four-helix TM1-kinked active conformation2–4. Accordingly, endogenous NINJ1 from primary macrophages is a dimer under steady-state conditions. Inactive dimers sequester the membrane rupture-inducing hydrophilic face of NINJ1 and occlude the binding site for kinked TM1 from neighbouring activated NINJ1 molecules. Mutagenesis studies in cells show that destabilization of inactive face-to-face dimers leads to NINJ1-mediated cell death, whereas stabilization of face-to-face dimers inhibits NINJ1 activity. Moreover, destabilizing mutations prompt spontaneous TM1 kink formation, a hallmark of NINJ1 activation. Collectively, our data demonstrate that dimeric NINJ1 is autoinhibited in trans to prevent unprovoked plasma membrane rupture and cell death.

Date: 2025
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DOI: 10.1038/s41586-024-08273-4

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