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- EMDB-16799: Cryo-EM structure of the NINJ1 filament -

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Basic information

Entry
Database: EMDB / ID: EMD-16799
TitleCryo-EM structure of the NINJ1 filament
Map data
Sample
  • Organelle or cellular component: NINJ1
    • Protein or peptide: Ninjurin-1
KeywordsPolymer / Membrane protein / Cell death
Function / homology
Function and homology information


: / cell adhesion mediator activity / regulation of monocyte chemotaxis / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / muscle cell differentiation / positive regulation of toll-like receptor 4 signaling pathway / tissue regeneration / programmed cell death / heterotypic cell-cell adhesion ...: / cell adhesion mediator activity / regulation of monocyte chemotaxis / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / muscle cell differentiation / positive regulation of toll-like receptor 4 signaling pathway / tissue regeneration / programmed cell death / heterotypic cell-cell adhesion / synaptic membrane / lipopolysaccharide binding / protein homooligomerization / positive regulation of inflammatory response / positive regulation of angiogenesis / nervous system development / angiogenesis / killing of cells of another organism / cell adhesion / inflammatory response / extracellular region
Similarity search - Function
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDegen MD / Hiller SH / Maier TM
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss Nanoscience Institute Switzerland
CitationJournal: Nature / Year: 2023
Title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.
Authors: Morris Degen / José Carlos Santos / Kristyna Pluhackova / Gonzalo Cebrero / Saray Ramos / Gytis Jankevicius / Ella Hartenian / Undina Guillerm / Stefania A Mari / Bastian Kohl / Daniel J ...Authors: Morris Degen / José Carlos Santos / Kristyna Pluhackova / Gonzalo Cebrero / Saray Ramos / Gytis Jankevicius / Ella Hartenian / Undina Guillerm / Stefania A Mari / Bastian Kohl / Daniel J Müller / Paul Schanda / Timm Maier / Camilo Perez / Christian Sieben / Petr Broz / Sebastian Hiller /
Abstract: Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event. Plasma membrane rupture was long thought to ...Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event. 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 (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.
History
DepositionMar 7, 2023-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16799.png

Downloads & links

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Map

FileDownload / File: emd_16799.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.12491487 - 0.21797712
Average (Standard dev.)0.0015063232 (±0.009171344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16799_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16799_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NINJ1

EntireName: NINJ1
Components
  • Organelle or cellular component: NINJ1
    • Protein or peptide: Ninjurin-1

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Supramolecule #1: NINJ1

SupramoleculeName: NINJ1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
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: 16.369932 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSDSGTEEYE LNGGLPPGTP GSPDASPARW GWRHGPINVN HYASKKSAAE SMLDIALLMA NASQLKAVVE QGPSFAFYVP LVVLISISL VLQIGVGVLL IFLVKYDLNN PAKHAKLDFL NNLATGLVFI IVVVNIFITA FGVQKPLMDM APQQ

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 20.95 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.05 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2, 3.3) / Number images used: 709840
FSC plot (resolution estimation)

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