8SZA

Cryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot.

Sahoo, B.Mou, Z.Liu, W.Dubyak, G.Dai, X.

(2025) Cell 188: 292-302.e11

  • DOI: https://doi.org/10.1016/j.cell.2024.11.021
  • Primary Citation of Related Structures:  
    8SZA, 8SZB

  • PubMed Abstract: 

    Ninjurin-1 (NINJ1) is an active executioner of plasma membrane rupture (PMR), a process previously thought to be a passive osmotic lysis event in lytic cell death. Ninjurin-2 (NINJ2) is a close paralog of NINJ1 but cannot mediate PMR. Using cryogenic electron microscopy (cryo-EM), we show that NINJ1 and NINJ2 both assemble into linear filaments that are hydrophobic on one side but hydrophilic on the other. This structural feature and other evidence point to a PMR mechanism by which NINJ1 filaments wrap around and solubilize membrane fragments and, less frequently, form pores in the plasma membrane. In contrast to the straight NINJ1 filament, the NINJ2 filament is curved toward the intracellular space, preventing its circularization or even assembly on a relatively flat membrane to mediate PMR. Mutagenesis studies further demonstrate that the NINJ2 filament curvature is induced by strong association with lipids, particularly a cholesterol molecule, at the cytoplasmic leaflet of the lipid bilayer.


  • Organizational Affiliation

    Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ninjurin-1
A, B, C, D, E
177Homo 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: 2.75 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesStartup Grant

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection
  • Version 1.2: 2024-12-18
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2024-12-25
    Changes: Data collection, Database references
  • Version 1.4: 2025-02-05
    Changes: Data collection, Database references