8UIP | pdb_00008uip

Cryo-EM Structure of Human Ninjurin1 curved oligomer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8UIP

This is version 1.1 of the entry. See complete history

Literature

NINJ1 mediates plasma membrane rupture by cutting and releasing membrane disks.

David, L.Borges, J.P.Hollingsworth, L.R.Volchuk, A.Jansen, I.Garlick, E.Steinberg, B.E.Wu, H.

(2024) Cell 187: 2224-2235.e16

  • DOI: https://doi.org/10.1016/j.cell.2024.03.008
  • Primary Citation Related Structures: 
    8UIP

  • PubMed Abstract: 

    The membrane protein NINJ1 mediates plasma membrane rupture in pyroptosis and other lytic cell death pathways. Here, we report the cryo-EM structure of a NINJ1 oligomer segmented from NINJ1 rings. Each NINJ1 subunit comprises amphipathic (⍺1, ⍺2) and transmembrane (TM) helices (⍺3, ⍺4) and forms a chain of subunits, mainly by the TM helices and ⍺1. ⍺3 and ⍺4 are kinked, and the Gly residues are important for function. The NINJ1 oligomer possesses a concave hydrophobic side that should face the membrane and a convex hydrophilic side formed by ⍺1 and ⍺2, presumably upon activation. This structural observation suggests that NINJ1 can form membrane disks, consistent with membrane fragmentation by recombinant NINJ1. Live-cell and super-resolution imaging uncover ring-like structures on the plasma membrane that are released into the culture supernatant. Released NINJ1 encircles a membrane inside, as shown by lipid staining. Therefore, NINJ1-mediated membrane disk formation is different from gasdermin-mediated pore formation, resulting in membrane loss and plasma membrane rupture.


  • Organizational Affiliation
    • Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 49.07 kDa 
  • Atom Count: 2,316 
  • Modeled Residue Count: 303 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ninjurin-1
A, B, C
152Homo 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: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesAI139914

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references