+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42301 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of Human Ninjurin1 curved oligomer | |||||||||
Map data | CryoEM map of human Ninjurin1 curved oligomer | |||||||||
Sample |
| |||||||||
Keywords | Ninjurin1 / NINJ1 / inflammation / inflammasome / pyroptosis / plasma membrane rupture / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information cell adhesion mediator activity / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / positive regulation of toll-like receptor 4 signaling pathway / tissue regeneration / muscle cell differentiation / programmed cell death / heterotypic cell-cell adhesion / pyroptotic inflammatory response / synaptic membrane ...cell adhesion mediator activity / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / positive regulation of toll-like receptor 4 signaling pathway / tissue regeneration / muscle cell differentiation / programmed cell death / heterotypic cell-cell adhesion / pyroptotic inflammatory response / 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 / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | David L / Wu H | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_42301.map.gz | 87.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-42301-v30.xml emd-42301.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_42301.png | 55 KB | ||
Filedesc metadata | emd-42301.cif.gz | 5.2 KB | ||
Others | emd_42301_half_map_1.map.gz emd_42301_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42301 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42301 | HTTPS FTP |
-Related structure data
Related structure data | 8uipMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_42301.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | CryoEM map of human Ninjurin1 curved oligomer | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half map B of human Ninjurin1 curved oligomer
File | emd_42301_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map B of human Ninjurin1 curved oligomer | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map A of human Ninjurin1 curved oligomer
File | emd_42301_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map A of human Ninjurin1 curved oligomer | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Ninjurin 1 ring oligomer
Entire | Name: Ninjurin 1 ring oligomer |
---|---|
Components |
|
-Supramolecule #1: Ninjurin 1 ring oligomer
Supramolecule | Name: Ninjurin 1 ring oligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ninjurin-1
Macromolecule | Name: Ninjurin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.356998 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw_1 (virus) |
Sequence | String: MDSGTEEYEL NGGLPPGTPG SPDASPARWG WRHGPINVNH YASKKSAAES MLDIALLMAN ASQLKAVVEQ GPSFAFYVPL VVLISISLV LQIGVGVLLI FLVKYDLNNP AKHAKLDFLN NLATGLVFII VVVNIFITAF GVQKPLMDMA PQQ UniProtKB: Ninjurin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
---|---|
Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 626231 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: BACKBONE TRACE |
---|---|
Output model | PDB-8uip: |