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Yorodumi- EMDB-40905: Cryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40905 | |||||||||
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Title | Cryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution | |||||||||
Map data | Cryo-EM Map of NINJ1 Filament | |||||||||
Sample |
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Keywords | NINJ1 Filament / Plasma Membrane Rupture Protein / Cholesterol Binding Protein / Lipid Binding Protein / Membrane Protein | |||||||||
Function / homology | Function and homology information ferroptosis / cell adhesion mediator activity / pyroptotic cell death / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / positive regulation of toll-like receptor 4 signaling pathway / programmed necrotic cell death / cytolysis / tissue regeneration / muscle cell differentiation ...ferroptosis / cell adhesion mediator activity / pyroptotic cell death / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / positive regulation of toll-like receptor 4 signaling pathway / programmed necrotic cell death / cytolysis / tissue regeneration / muscle cell differentiation / cellular hyperosmotic response / 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 / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||
Authors | Sahoo B / Dai X | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Biorxiv / Year: 2023 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40905.map.gz | 168 MB | EMDB map data format | |
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Header (meta data) | emd-40905-v30.xml emd-40905.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40905_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_40905.png | 96.7 KB | ||
Filedesc metadata | emd-40905.cif.gz | 5.1 KB | ||
Others | emd_40905_half_map_1.map.gz emd_40905_half_map_2.map.gz | 165.4 MB 165.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40905 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40905 | HTTPS FTP |
-Validation report
Summary document | emd_40905_validation.pdf.gz | 950.9 KB | Display | EMDB validaton report |
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Full document | emd_40905_full_validation.pdf.gz | 950.4 KB | Display | |
Data in XML | emd_40905_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | emd_40905_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40905 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40905 | HTTPS FTP |
-Related structure data
Related structure data | 8szaMC 8szbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40905.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM Map of NINJ1 Filament | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.66 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM Half Map A of NINJ1 Filament
File | emd_40905_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM Half Map A of NINJ1 Filament | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM Half Map B of NINJ1 Filament
File | emd_40905_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM Half Map B of NINJ1 Filament | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ninjurin-1 in complex with Cholesterol
Entire | Name: Ninjurin-1 in complex with Cholesterol |
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Components |
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-Supramolecule #1: Ninjurin-1 in complex with Cholesterol
Supramolecule | Name: Ninjurin-1 in complex with Cholesterol / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ninjurin-1
Macromolecule | Name: Ninjurin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 19.276896 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDYKDHDGDY KDHDIDYKDD DDKGSGDSGT EEYELNGGLP PGTPGSPDAS PARWGWRHGP INVNHYASKK SAAESMLDIA LLMANASQL KAVVEQGPSF AFYVPLVVLI SISLVLQIGV GVLLIFLVKY DLNNPAKHAK LDFLNNLATG LVFIIVVVNI F ITAFGVQK PLMDMAPQQ UniProtKB: Ninjurin-1 |
-Macromolecule #2: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 6 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 1.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |