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Open data
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Basic information
Entry | Database: PDB / ID: 8sza | ||||||
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Title | Cryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution | ||||||
![]() | Ninjurin-1 | ||||||
![]() | MEMBRANE PROTEIN / NINJ1 Filament / Plasma Membrane Rupture Protein / Cholesterol Binding Protein / Lipid Binding Protein | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||
![]() | Sahoo, B. / Dai, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot Authors: Sahoo, B. / Mou, Z. / Liu, W. / Dubyak, G. / Dai, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.7 KB | Display | ![]() |
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PDB format | ![]() | 100.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 37 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 40905MC ![]() 8szbC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 19276.896 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-CLR / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Ninjurin-1 in complex with Cholesterol / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282383 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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