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- PDB-8szb: Cryo-EM Structure of NINJ2 Filament at 3.07 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 8szb
TitleCryo-EM Structure of NINJ2 Filament at 3.07 Angstrom Resolution
ComponentsNinjurin-2
KeywordsMEMBRANE PROTEIN / NINJ2 Filament / NINJ1 Paralog Protein / Cholesterol Binding Protein / Lipid Binding Protein
Function / homologyNinjurin / Ninjurin / neuron cell-cell adhesion / tissue regeneration / nervous system development / cell adhesion / plasma membrane / CHOLESTEROL / Ninjurin-2
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 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
F: Ninjurin-2
A: Ninjurin-2
C: Ninjurin-2
E: Ninjurin-2
D: Ninjurin-2
B: Ninjurin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,01112
Polymers111,6916
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-2 / Nerve injury-induced protein 2


Mass: 18615.115 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NINJ2 / Production host: Homo sapiens (human) / References: UniProt: Q9NZG7
#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-2 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: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 375439 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025052
ELECTRON MICROSCOPYf_angle_d0.4466912
ELECTRON MICROSCOPYf_dihedral_angle_d6.607696
ELECTRON MICROSCOPYf_chiral_restr0.034906
ELECTRON MICROSCOPYf_plane_restr0.003798

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