SMTL ID : 7xl8.1

Human Cx36/GJD2 (N-terminal deletion mutant) gap junction channel in soybean lipids (D6 symmetry)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

84 x MC3: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

MC3.1: 6 residues within 4Å: Chain A: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.2 Ligand excluded by PLIP MC3.2: 5 residues within 4Å: Chain A: V.248, A.252 Ligands: MC3.1, MC3.3, MC3.8 Ligand excluded by PLIP MC3.3: 8 residues within 4Å: Chain A: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.2, MC3.8, MC3.9 Ligand excluded by PLIP MC3.4: 5 residues within 4Å: Chain A: F.74 Ligands: MC3.5, MC3.6, MC3.41, MC3.42 Ligand excluded by PLIP MC3.5: 11 residues within 4Å: Chain A: R.62, P.65, I.66, Y.71, F.74, L.213 Chain F: T.241, V.245 Ligands: MC3.4, MC3.6, MC3.42 Ligand excluded by PLIP MC3.6: 9 residues within 4Å: Chain A: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.4, MC3.5, MC3.7 Ligand excluded by PLIP MC3.7: 5 residues within 4Å: Chain A: G.205, V.208, G.209, F.212 Ligands: MC3.6 Ligand excluded by PLIP MC3.8: 4 residues within 4Å: Ligands: MC3.2, MC3.3, MC3.9, MC3.10 Ligand excluded by PLIP MC3.9: 11 residues within 4Å: Chain A: T.241, V.245 Chain B: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.3, MC3.8, MC3.10 Ligand excluded by PLIP MC3.10: 9 residues within 4Å: Chain B: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.8, MC3.9, MC3.11 Ligand excluded by PLIP MC3.11: 5 residues within 4Å: Chain B: G.205, V.208, G.209, F.212 Ligands: MC3.10 Ligand excluded by PLIP MC3.12: 6 residues within 4Å: Chain B: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.13 Ligand excluded by PLIP MC3.13: 5 residues within 4Å: Chain B: V.248, A.252 Ligands: MC3.12, MC3.14, MC3.15 Ligand excluded by PLIP MC3.14: 8 residues within 4Å: Chain B: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.13, MC3.15, MC3.16 Ligand excluded by PLIP MC3.15: 4 residues within 4Å: Ligands: MC3.13, MC3.14, MC3.16, MC3.17 Ligand excluded by PLIP MC3.16: 11 residues within 4Å: Chain B: T.241, V.245 Chain C: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.14, MC3.15, MC3.17 Ligand excluded by PLIP MC3.17: 9 residues within 4Å: Chain C: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.15, MC3.16, MC3.18 Ligand excluded by PLIP MC3.18: 5 residues within 4Å: Chain C: G.205, V.208, G.209, F.212 Ligands: MC3.17 Ligand excluded by PLIP MC3.19: 6 residues within 4Å: Chain C: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.20 Ligand excluded by PLIP MC3.20: 5 residues within 4Å: Chain C: V.248, A.252 Ligands: MC3.19, MC3.21, MC3.22 Ligand excluded by PLIP MC3.21: 8 residues within 4Å: Chain C: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.20, MC3.22, MC3.23 Ligand excluded by PLIP MC3.22: 4 residues within 4Å: Ligands: MC3.20, MC3.21, MC3.23, MC3.24 Ligand excluded by PLIP MC3.23: 11 residues within 4Å: Chain C: T.241, V.245 Chain D: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.21, MC3.22, MC3.24 Ligand excluded by PLIP MC3.24: 9 residues within 4Å: Chain D: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.22, MC3.23, MC3.25 Ligand excluded by PLIP MC3.25: 5 residues within 4Å: Chain D: G.205, V.208, G.209, F.212 Ligands: MC3.24 Ligand excluded by PLIP MC3.26: 6 residues within 4Å: Chain D: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.27 Ligand excluded by PLIP MC3.27: 5 residues within 4Å: Chain D: V.248, A.252 Ligands: MC3.26, MC3.28, MC3.29 Ligand excluded by PLIP MC3.28: 8 residues within 4Å: Chain D: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.27, MC3.29, MC3.30 Ligand excluded by PLIP MC3.29: 4 residues within 4Å: Ligands: MC3.27, MC3.28, MC3.30, MC3.31 Ligand excluded by PLIP MC3.30: 11 residues within 4Å: Chain D: T.241, V.245 Chain E: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.28, MC3.29, MC3.31 Ligand excluded by PLIP MC3.31: 9 residues within 4Å: Chain E: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.29, MC3.30, MC3.32 Ligand excluded by PLIP MC3.32: 5 residues within 4Å: Chain E: G.205, V.208, G.209, F.212 Ligands: MC3.31 Ligand excluded by PLIP MC3.33: 6 residues within 4Å: Chain E: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.34 Ligand excluded by PLIP MC3.34: 5 residues within 4Å: Chain E: V.248, A.252 Ligands: MC3.33, MC3.35, MC3.36 Ligand excluded by PLIP MC3.35: 8 residues within 4Å: Chain E: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.34, MC3.36, MC3.37 Ligand excluded by PLIP MC3.36: 5 residues within 4Å: Chain F: F.74 Ligands: MC3.34, MC3.35, MC3.37, MC3.38 Ligand excluded by PLIP MC3.37: 11 residues within 4Å: Chain E: T.241, V.245 Chain F: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.35, MC3.36, MC3.38 Ligand excluded by PLIP MC3.38: 9 residues within 4Å: Chain F: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.36, MC3.37, MC3.39 Ligand excluded by PLIP MC3.39: 5 residues within 4Å: Chain F: G.205, V.208, G.209, F.212 Ligands: MC3.38 Ligand excluded by PLIP MC3.40: 6 residues within 4Å: Chain F: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.41 Ligand excluded by PLIP MC3.41: 5 residues within 4Å: Chain F: V.248, A.252 Ligands: MC3.4, MC3.40, MC3.42 Ligand excluded by PLIP MC3.42: 8 residues within 4Å: Chain F: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.4, MC3.5, MC3.41 Ligand excluded by PLIP MC3.43: 6 residues within 4Å: Chain G: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.44 Ligand excluded by PLIP MC3.44: 5 residues within 4Å: Chain G: V.248, A.252 Ligands: MC3.43, MC3.45, MC3.50 Ligand excluded by PLIP MC3.45: 8 residues within 4Å: Chain G: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.44, MC3.50, MC3.51 Ligand excluded by PLIP MC3.46: 4 residues within 4Å: Ligands: MC3.47, MC3.48, MC3.83, MC3.84 Ligand excluded by PLIP MC3.47: 11 residues within 4Å: Chain G: R.62, P.65, I.66, Y.71, F.74, L.213 Chain L: T.241, V.245 Ligands: MC3.46, MC3.48, MC3.84 Ligand excluded by PLIP MC3.48: 9 residues within 4Å: Chain G: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.46, MC3.47, MC3.49 Ligand excluded by PLIP MC3.49: 5 residues within 4Å: Chain G: G.205, V.208, G.209, F.212 Ligands: MC3.48 Ligand excluded by PLIP MC3.50: 5 residues within 4Å: Chain H: F.74 Ligands: MC3.44, MC3.45, MC3.51, MC3.52 Ligand excluded by PLIP MC3.51: 11 residues within 4Å: Chain G: T.241, V.245 Chain H: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.45, MC3.50, MC3.52 Ligand excluded by PLIP MC3.52: 9 residues within 4Å: Chain H: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.50, MC3.51, MC3.53 Ligand excluded by PLIP MC3.53: 5 residues within 4Å: Chain H: G.205, V.208, G.209, F.212 Ligands: MC3.52 Ligand excluded by PLIP MC3.54: 6 residues within 4Å: Chain H: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.55 Ligand excluded by PLIP MC3.55: 5 residues within 4Å: Chain H: V.248, A.252 Ligands: MC3.54, MC3.56, MC3.57 Ligand excluded by PLIP MC3.56: 8 residues within 4Å: Chain H: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.55, MC3.57, MC3.58 Ligand excluded by PLIP MC3.57: 4 residues within 4Å: Ligands: MC3.55, MC3.56, MC3.58, MC3.59 Ligand excluded by PLIP MC3.58: 11 residues within 4Å: Chain H: T.241, V.245 Chain I: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.56, MC3.57, MC3.59 Ligand excluded by PLIP MC3.59: 9 residues within 4Å: Chain I: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.57, MC3.58, MC3.60 Ligand excluded by PLIP MC3.60: 5 residues within 4Å: Chain I: G.205, V.208, G.209, F.212 Ligands: MC3.59 Ligand excluded by PLIP MC3.61: 6 residues within 4Å: Chain I: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.62 Ligand excluded by PLIP MC3.62: 5 residues within 4Å: Chain I: V.248, A.252 Ligands: MC3.61, MC3.63, MC3.64 Ligand excluded by PLIP MC3.63: 8 residues within 4Å: Chain I: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.62, MC3.64, MC3.65 Ligand excluded by PLIP MC3.64: 4 residues within 4Å: Ligands: MC3.62, MC3.63, MC3.65, MC3.66 Ligand excluded by PLIP MC3.65: 11 residues within 4Å: Chain I: T.241, V.245 Chain J: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.63, MC3.64, MC3.66 Ligand excluded by PLIP MC3.66: 9 residues within 4Å: Chain J: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.64, MC3.65, MC3.67 Ligand excluded by PLIP MC3.67: 5 residues within 4Å: Chain J: G.205, V.208, G.209, F.212 Ligands: MC3.66 Ligand excluded by PLIP MC3.68: 6 residues within 4Å: Chain J: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.69 Ligand excluded by PLIP MC3.69: 5 residues within 4Å: Chain J: V.248, A.252 Ligands: MC3.68, MC3.70, MC3.71 Ligand excluded by PLIP MC3.70: 8 residues within 4Å: Chain J: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.69, MC3.71, MC3.72 Ligand excluded by PLIP MC3.71: 4 residues within 4Å: Ligands: MC3.69, MC3.70, MC3.72, MC3.73 Ligand excluded by PLIP MC3.72: 11 residues within 4Å: Chain J: T.241, V.245 Chain K: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.70, MC3.71, MC3.73 Ligand excluded by PLIP MC3.73: 9 residues within 4Å: Chain K: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.71, MC3.72, MC3.74 Ligand excluded by PLIP MC3.74: 5 residues within 4Å: Chain K: G.205, V.208, G.209, F.212 Ligands: MC3.73 Ligand excluded by PLIP MC3.75: 6 residues within 4Å: Chain K: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.76 Ligand excluded by PLIP MC3.76: 5 residues within 4Å: Chain K: V.248, A.252 Ligands: MC3.75, MC3.77, MC3.78 Ligand excluded by PLIP MC3.77: 8 residues within 4Å: Chain K: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.76, MC3.78, MC3.79 Ligand excluded by PLIP MC3.78: 4 residues within 4Å: Ligands: MC3.76, MC3.77, MC3.79, MC3.80 Ligand excluded by PLIP MC3.79: 11 residues within 4Å: Chain K: T.241, V.245 Chain L: R.62, P.65, I.66, Y.71, F.74, L.213 Ligands: MC3.77, MC3.78, MC3.80 Ligand excluded by PLIP MC3.80: 9 residues within 4Å: Chain L: Y.71, G.205, F.206, G.209, F.212, L.213 Ligands: MC3.78, MC3.79, MC3.81 Ligand excluded by PLIP MC3.81: 5 residues within 4Å: Chain L: G.205, V.208, G.209, F.212 Ligands: MC3.80 Ligand excluded by PLIP MC3.82: 6 residues within 4Å: Chain L: F.216, S.217, V.248, F.251, A.252 Ligands: MC3.83 Ligand excluded by PLIP MC3.83: 5 residues within 4Å: Chain L: V.248, A.252 Ligands: MC3.46, MC3.82, MC3.84 Ligand excluded by PLIP MC3.84: 8 residues within 4Å: Chain L: T.241, T.244, V.245, V.248, F.249 Ligands: MC3.46, MC3.47, MC3.83 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S.N. et al., Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel. Nat Commun (2023)

Release Date

2023-08-30

Peptides

Gap junction delta-2 protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Membrane

We predict this structure to be a membrane protein.
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Gap junction delta-2 protein