8CQR

Cryo-EM structure of the NINJ1 filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of NINJ1-mediated plasma membrane rupture in cell death.

Degen, M.Santos, J.C.Pluhackova, K.Cebrero, G.Ramos, S.Jankevicius, G.Hartenian, E.Guillerm, U.Mari, S.A.Kohl, B.Muller, D.J.Schanda, P.Maier, T.Perez, C.Sieben, C.Broz, P.Hiller, S.

(2023) Nature 618: 1065-1071

  • DOI: https://doi.org/10.1038/s41586-023-05991-z
  • Primary Citation of Related Structures:  
    8CQR

  • PubMed Abstract: 

    Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event 1-7 . Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-1 8 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.


  • Organizational Affiliation

    Biozentrum, University of Basel, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ninjurin-1153Homo sapiensMutation(s): 0 
Gene Names: NINJ1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92982 (Homo sapiens)
Explore Q92982 
Go to UniProtKB:  Q92982
PHAROS:  Q92982
GTEx:  ENSG00000131669 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92982
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2, 3.3
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss Nanoscience InstituteSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references
  • Version 1.3: 2023-07-12
    Changes: Database references