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- PDB-8sza: Cryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 8sza
TitleCryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution
ComponentsNinjurin-1
KeywordsMEMBRANE PROTEIN / NINJ1 Filament / Plasma Membrane Rupture Protein / Cholesterol Binding Protein / Lipid Binding Protein
Function / homology
Function and homology information


ferroptosis / cell adhesion mediator activity / pyroptotic cell death / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / cytolysis / positive regulation of toll-like receptor 4 signaling pathway / programmed necrotic cell death / tissue regeneration / muscle cell differentiation ...ferroptosis / cell adhesion mediator activity / pyroptotic cell death / leukocyte chemotaxis involved in inflammatory response / membrane destabilizing activity / cytolysis / positive regulation of toll-like receptor 4 signaling pathway / programmed necrotic cell death / 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
CHOLESTEROL / Ninjurin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSahoo, B. / Dai, X.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateStartup Grant United States
CitationJournal: 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
DepositionMay 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ninjurin-1
B: Ninjurin-1
C: Ninjurin-1
D: Ninjurin-1
E: Ninjurin-1
F: Ninjurin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,98112
Polymers115,6616
Non-polymers2,3206
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Ninjurin-1 / Nerve injury-induced protein 1


Mass: 19276.896 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NINJ1 / Production host: Homo sapiens (human) / References: UniProt: Q92982
#2: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ninjurin-1 in complex with Cholesterol / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282383 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024908
ELECTRON MICROSCOPYf_angle_d0.5836720
ELECTRON MICROSCOPYf_dihedral_angle_d4.217678
ELECTRON MICROSCOPYf_chiral_restr0.033870
ELECTRON MICROSCOPYf_plane_restr0.002786

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