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Open data
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Basic information
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Title | Cryo-EM Structure of Human Ninjurin1 curved oligomer | |||||||||
![]() | CryoEM map of human Ninjurin1 curved oligomer | |||||||||
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![]() | Ninjurin1 / NINJ1 / ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() cell adhesion mediator activity / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / positive regulation of toll-like receptor 4 signaling pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | David L / Wu H | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 87.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
Images | ![]() | 55 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() | 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uipMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | CryoEM map of human Ninjurin1 curved oligomer | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B of human Ninjurin1 curved oligomer
File | emd_42301_half_map_1.map | ||||||||||||
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Annotation | Half map B of human Ninjurin1 curved oligomer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of human Ninjurin1 curved oligomer
File | emd_42301_half_map_2.map | ||||||||||||
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Annotation | Half map A of human Ninjurin1 curved oligomer | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Ninjurin 1 ring oligomer
Entire | Name: Ninjurin 1 ring oligomer |
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Components |
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-Supramolecule #1: Ninjurin 1 ring oligomer
Supramolecule | Name: Ninjurin 1 ring oligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Ninjurin-1
Macromolecule | Name: Ninjurin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.356998 KDa |
Recombinant expression | Organism: ![]() |
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 | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.3 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 626231 |
-Atomic model buiding 1
Refinement | Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-8uip: |