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- PDB-8sza: Cryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 8sza
TitleCryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution
ComponentsNinjurin-1
KeywordsMEMBRANE PROTEIN / NINJ1 Filament / Plasma Membrane Rupture Protein / Cholesterol Binding Protein / Lipid Binding Protein
Function / homology
Function and homology information


ferroptosis / pyroptotic cell death / membrane destabilizing activity / cytolysis / leukocyte chemotaxis involved in inflammatory response / cell adhesion mediator activity / positive regulation of toll-like receptor 4 signaling pathway / programmed necrotic cell death / tissue regeneration / muscle cell differentiation ...ferroptosis / pyroptotic cell death / membrane destabilizing activity / cytolysis / leukocyte chemotaxis involved in inflammatory response / cell adhesion mediator activity / positive regulation of toll-like receptor 4 signaling pathway / programmed necrotic cell death / tissue regeneration / muscle cell differentiation / cellular hyperosmotic response / heterotypic cell-cell adhesion / synaptic membrane / lipopolysaccharide binding / protein homooligomerization / positive regulation of angiogenesis / positive regulation of inflammatory response / nervous system development / angiogenesis / killing of cells of another organism / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
CHOLESTEROL / Ninjurin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSahoo, B. / Dai, X.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateStartup Grant United States
CitationJournal: Cell / Year: 2025
Title: How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot.
Authors: Bibekananda Sahoo / Zongjun Mou / Wei Liu / George Dubyak / Xinghong Dai /
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 ...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.
History
DepositionMay 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Dec 18, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Dec 25, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.4Feb 5, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ninjurin-1
B: Ninjurin-1
C: Ninjurin-1
D: Ninjurin-1
E: Ninjurin-1
F: Ninjurin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,98112
Polymers115,6616
Non-polymers2,3206
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Ninjurin-1 / Nerve injury-induced protein 1


Mass: 19276.896 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NINJ1 / Production host: Homo sapiens (human) / References: UniProt: Q92982
#2: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ninjurin-1 in complex with Cholesterol / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282383 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024908
ELECTRON MICROSCOPYf_angle_d0.5836720
ELECTRON MICROSCOPYf_dihedral_angle_d4.217678
ELECTRON MICROSCOPYf_chiral_restr0.033870
ELECTRON MICROSCOPYf_plane_restr0.002786

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