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- EMDB-42301: Cryo-EM Structure of Human Ninjurin1 curved oligomer -

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Basic information

Entry
Database: EMDB / ID: EMD-42301
TitleCryo-EM Structure of Human Ninjurin1 curved oligomer
Map dataCryoEM map of human Ninjurin1 curved oligomer
Sample
  • Complex: Ninjurin 1 ring oligomer
    • Protein or peptide: Ninjurin-1
KeywordsNinjurin1 / NINJ1 / inflammation / inflammasome / pyroptosis / plasma membrane rupture / IMMUNE SYSTEM
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: 4.3 Å
AuthorsDavid L / Wu H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)AI139914 United States
CitationJournal: Cell / Year: 2024
Title: NINJ1 mediates plasma membrane rupture by cutting and releasing membrane disks.
Authors: Liron David / Jazlyn P Borges / L Robert Hollingsworth / Allen Volchuk / Isabelle Jansen / Evelyn Garlick / Benjamin E Steinberg / Hao Wu /
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. ...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.
History
DepositionOct 10, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42301.png

Downloads & links

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Map

FileDownload / File: emd_42301.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of human Ninjurin1 curved oligomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.07814311 - 1.872719
Average (Standard dev.)0.0012914019 (±0.022980817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B of human Ninjurin1 curved oligomer

Fileemd_42301_half_map_1.map
AnnotationHalf map B of human Ninjurin1 curved oligomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of human Ninjurin1 curved oligomer

Fileemd_42301_half_map_2.map
AnnotationHalf map A of human Ninjurin1 curved oligomer
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 ring oligomer

EntireName: Ninjurin 1 ring oligomer
Components
  • Complex: Ninjurin 1 ring oligomer
    • Protein or peptide: Ninjurin-1

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Supramolecule #1: Ninjurin 1 ring oligomer

SupramoleculeName: Ninjurin 1 ring oligomer / type: complex / 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: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.356998 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw_1 (virus)
SequenceString:
MDSGTEEYEL NGGLPPGTPG SPDASPARWG WRHGPINVNH YASKKSAAES MLDIALLMAN ASQLKAVVEQ GPSFAFYVPL VVLISISLV LQIGVGVLLI FLVKYDLNNP AKHAKLDFLN NLATGLVFII VVVNIFITAF GVQKPLMDMA PQQ

UniProtKB: Ninjurin-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
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: 51.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 626231
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-8uip:
Cryo-EM Structure of Human Ninjurin1 curved oligomer

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