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- EMDB-40905: Cryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-40905
TitleCryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution
Map dataCryo-EM Map of NINJ1 Filament
Sample
  • Organelle or cellular component: Ninjurin-1 in complex with Cholesterol
    • Protein or peptide: Ninjurin-1
  • Ligand: CHOLESTEROL
KeywordsNINJ1 Filament / Plasma Membrane Rupture Protein / Cholesterol Binding Protein / Lipid Binding Protein / Membrane Protein
Function / homology
Function and homology information


ferroptosis / pyroptotic cell death / cell adhesion mediator activity / membrane destabilizing activity / leukocyte chemotaxis involved in inflammatory response / cytolysis / positive regulation of toll-like receptor 4 signaling pathway / tissue regeneration / programmed necrotic cell death / muscle cell differentiation ...ferroptosis / pyroptotic cell death / cell adhesion mediator activity / membrane destabilizing activity / leukocyte chemotaxis involved in inflammatory response / cytolysis / positive regulation of toll-like receptor 4 signaling pathway / tissue regeneration / programmed necrotic cell death / muscle cell differentiation / cellular hyperosmotic response / heterotypic cell-cell adhesion / lipopolysaccharide binding / synaptic membrane / protein homooligomerization / positive regulation of inflammatory response / positive regulation of angiogenesis / nervous system development / angiogenesis / killing of cells of another organism / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSahoo B / Dai X
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40905.png

Downloads & links

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Map

FileDownload / File: emd_40905.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM Map of NINJ1 Filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 360 pix.
= 237.6 Å		0.66 Å/pix.
x 360 pix.
= 237.6 Å		0.66 Å/pix.
x 360 pix.
= 237.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.64254934 - 0.92060024
Average (Standard dev.)0.0013399561 (±0.025067069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM Half Map A of NINJ1 Filament

Fileemd_40905_half_map_1.map
AnnotationCryo-EM Half Map A of NINJ1 Filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM Half Map B of NINJ1 Filament

Fileemd_40905_half_map_2.map
AnnotationCryo-EM Half Map B of NINJ1 Filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ninjurin-1 in complex with Cholesterol

EntireName: Ninjurin-1 in complex with Cholesterol
Components
  • Organelle or cellular component: Ninjurin-1 in complex with Cholesterol
    • Protein or peptide: Ninjurin-1
  • Ligand: CHOLESTEROL

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Supramolecule #1: Ninjurin-1 in complex with Cholesterol

SupramoleculeName: Ninjurin-1 in complex with Cholesterol / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ninjurin-1

MacromoleculeName: Ninjurin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.276896 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDYKDHDGDY KDHDIDYKDD DDKGSGDSGT EEYELNGGLP PGTPGSPDAS PARWGWRHGP INVNHYASKK SAAESMLDIA LLMANASQL KAVVEQGPSF AFYVPLVVLI SISLVLQIGV GVLLIFLVKY DLNNPAKHAK LDFLNNLATG LVFIIVVVNI F ITAFGVQK PLMDMAPQQ

UniProtKB: Ninjurin-1

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282383
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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