9BIA
Cryo-EM structure of NINJ1 K45Q bound to Nb538
Summary for 9BIA
| Entry DOI | 10.2210/pdb9bia/pdb |
| EMDB information | 44585 |
| Descriptor | Ninjurin-1, Nb538 (2 entities in total) |
| Functional Keywords | inactive-state, membrane rupture, complex, membrane protein |
| Biological source | Mus musculus (house mouse) More |
| Total number of polymer chains | 6 |
| Total formula weight | 104846.24 |
| Authors | Pourmal, S.,Johnson, M.C.,Deshpande, I. (deposition date: 2024-04-23, release date: 2024-10-16, Last modification date: 2025-04-16) |
| Primary citation | Pourmal, S.,Truong, M.E.,Johnson, M.C.,Yang, Y.,Zhou, L.,Alegre, K.,Stowe, I.B.,Gupta, S.,Chen, P.A.,Zhang, Y.,Rohou, A.,Newton, K.,Kayagaki, N.,Dixit, V.M.,Deshpande, I. Autoinhibition of dimeric NINJ1 prevents plasma membrane rupture. Nature, 637:446-452, 2025 Cited by PubMed 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), which polymerizes and ruptures the membrane via its hydrophilic face. 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 conformation. 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. PubMed: 39476863DOI: 10.1038/s41586-024-08273-4 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3 Å) |
Structure validation
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