SMTL ID : 8sza.1

Cryo-EM Structure of NINJ1 Filament at 2.75 Angstrom Resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 8 residues within 4Å: Chain B: L.122, F.125, Y.129, L.143 Chain D: F.142 Chain E: F.125 Ligands: CLR.3, CLR.5 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: B:F.125, B:L.143, D:F.142, E:F.125 Hydrogen bonds: B:Y.129 CLR.2: 5 residues within 4Å: Chain C: L.122, F.125, Y.129 Chain D: F.125 Ligands: CLR.3 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.122, C:L.122, C:F.125, D:F.125 Hydrogen bonds: C:Y.129 CLR.3: 7 residues within 4Å: Chain B: F.142 Chain D: L.122, F.125, Y.129, L.143 Ligands: CLR.1, CLR.2 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.122, D:L.122, D:F.125, B:F.142 CLR.4: 7 residues within 4Å: Chain A: L.122, F.125, Y.129, L.143 Chain E: F.142 Ligands: CLR.5, CLR.6 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:F.142, E:F.142, A:F.125, A:L.143, A:L.143 CLR.5: 7 residues within 4Å: Chain A: F.142 Chain E: L.122, F.125, Y.129, L.143 Ligands: CLR.1, CLR.4 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:L.122, E:F.125, E:L.143, A:F.142 Hydrogen bonds: E:Y.129 CLR.6: 5 residues within 4Å: Chain A: F.125 Chain F: L.122, F.125, Y.129 Ligands: CLR.4 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain F Hydrophobic interactions: A:F.125, F:L.122, F:L.122, F:F.125 Hydrogen bonds: F:Y.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sahoo, B. et al., How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot. Biorxiv (2023)

Release Date

2023-06-14

Peptides

Ninjurin-1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Ninjurin-1