SMTL ID : 6w6o.1

NaChBac-Nav1.7VSDII chimera and HWTX-IV complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

12 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 11 residues within 4Å: Chain A: F.205, A.206, P.209, W.210, W.212 Chain G: L.151, Q.181, L.184, L.185, F.188 Ligands: POV.7 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain A Hydrophobic interactions: G:L.151, G:L.185, A:W.210, A:W.212, A:W.212, A:W.212 POV.2: 11 residues within 4Å: Chain A: F.157, F.161, L.168, E.207, V.208, W.210, S.211, L.213, I.221 Chain G: S.113, L.124 7 PLIP interactions: 1 interactions with chain G, 6 interactions with chain A Hydrogen bonds: G:S.113 Hydrophobic interactions: A:F.157, A:F.157, A:F.161, A:W.210, A:L.213, A:I.221 POV.3: 13 residues within 4Å: Chain A: L.34, I.42, Y.45, R.47, I.48 Chain C: S.155, I.156, F.158, Y.159, L.180, Q.181, L.184 Ligands: POV.8 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:L.34, A:I.42, C:I.156, C:F.158, C:Y.159, C:L.180, C:L.184, C:L.184 POV.4: 11 residues within 4Å: Chain A: L.151, Q.181, L.184, L.185, F.188 Chain C: F.205, A.206, P.209, W.210, W.212 Ligands: POV.10 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.151, A:L.185, C:W.210, C:W.212, C:W.212, C:W.212 POV.5: 11 residues within 4Å: Chain A: S.113, L.124 Chain C: F.157, F.161, L.168, E.207, V.208, W.210, S.211, L.213, I.221 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.157, C:F.157, C:F.161, C:W.210, C:L.213, C:I.221 Hydrogen bonds: A:S.113 POV.6: 13 residues within 4Å: Chain C: L.34, I.42, Y.45, R.47, I.48 Chain E: S.155, I.156, F.158, Y.159, L.180, Q.181, L.184 Ligands: POV.11 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:I.156, E:F.158, E:Y.159, E:L.180, E:L.184, E:L.184, C:L.34, C:I.42 POV.7: 13 residues within 4Å: Chain E: L.34, I.42, Y.45, R.47, I.48 Chain G: S.155, I.156, F.158, Y.159, L.180, Q.181, L.184 Ligands: POV.1 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain E Hydrophobic interactions: G:I.156, G:F.158, G:L.180, G:L.184, G:L.184, E:L.34, E:I.42 POV.8: 11 residues within 4Å: Chain C: L.151, Q.181, L.184, L.185, F.188 Chain E: F.205, A.206, P.209, W.210, W.212 Ligands: POV.3 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:W.210, E:W.212, E:W.212, E:W.212, C:L.151, C:L.185 POV.9: 11 residues within 4Å: Chain C: S.113, L.124 Chain E: F.157, F.161, L.168, E.207, V.208, W.210, S.211, L.213, I.221 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.157, E:F.157, E:F.161, E:W.210, E:L.213, E:I.221 Hydrogen bonds: C:S.113 POV.10: 13 residues within 4Å: Chain A: S.155, I.156, F.158, Y.159, L.180, Q.181, L.184 Chain G: L.34, I.42, Y.45, R.47, I.48 Ligands: POV.4 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:I.156, A:F.158, A:Y.159, A:L.180, A:L.184, A:L.184, G:L.34, G:I.42 POV.11: 11 residues within 4Å: Chain E: L.151, Q.181, L.184, L.185, F.188 Chain G: F.205, A.206, P.209, W.210, W.212 Ligands: POV.6 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain G Hydrophobic interactions: E:L.151, E:L.185, G:W.210, G:W.212, G:W.212, G:W.212 POV.12: 11 residues within 4Å: Chain E: S.113, L.124 Chain G: F.157, F.161, L.168, E.207, V.208, W.210, S.211, L.213, I.221 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:F.157, G:F.157, G:F.161, G:W.210, G:L.213, G:I.221 Hydrogen bonds: E:S.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, S. et al., Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na + channels in nanodisc. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-06-24

Peptides

NaChBac-Nav1.7VSDII chimera: ACEG
Huwentoxin-IV: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
F

G
H

B
C

D
E

F
G

H
I

Membrane

We predict this structure to be a membrane protein.
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NaChBac-Nav1.7VSDII chimera

Huwentoxin-IV

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