SMTL ID : 7xnv.1

Structurally hetero-junctional human Cx36/GJD2 gap junction channel in soybean lipids (C6 symmetry)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

MC3.1: 8 residues within 4Å: Chain A: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.2, MC3.3 Ligand excluded by PLIP MC3.2: 4 residues within 4Å: Chain A: F.223, S.224 Ligands: MC3.1, MC3.3 Ligand excluded by PLIP MC3.3: 4 residues within 4Å: Chain A: V.255 Ligands: MC3.1, MC3.2, MC3.59 Ligand excluded by PLIP MC3.4: 4 residues within 4Å: Chain A: E.8 Chain F: L.10, V.98 Ligands: MC3.5 Ligand excluded by PLIP MC3.5: 7 residues within 4Å: Chain A: V.15, R.24, T.28, V.31, I.32 Chain F: V.98 Ligands: MC3.4 Ligand excluded by PLIP MC3.6: 5 residues within 4Å: Chain A: P.72, I.73, Y.78, F.81 Ligands: MC3.7 Ligand excluded by PLIP MC3.7: 6 residues within 4Å: Chain A: G.212, G.216, L.220 Ligands: MC3.6, MC3.8, MC3.9 Ligand excluded by PLIP MC3.8: 3 residues within 4Å: Chain A: G.212, F.219 Ligands: MC3.7 Ligand excluded by PLIP MC3.9: 2 residues within 4Å: Ligands: MC3.7, MC3.14 Ligand excluded by PLIP MC3.10: 3 residues within 4Å: Chain A: T.88, F.198, I.201 Ligand excluded by PLIP MC3.11: 6 residues within 4Å: Chain A: C.92, T.95, F.198 Chain B: M.21, I.25, T.28 Ligand excluded by PLIP MC3.12: 8 residues within 4Å: Chain B: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.13, MC3.14 Ligand excluded by PLIP MC3.13: 5 residues within 4Å: Chain B: F.223, S.224, A.259 Ligands: MC3.12, MC3.14 Ligand excluded by PLIP MC3.14: 4 residues within 4Å: Chain B: V.255 Ligands: MC3.9, MC3.12, MC3.13 Ligand excluded by PLIP MC3.15: 4 residues within 4Å: Chain A: L.10 Chain B: E.8, E.12 Ligands: MC3.16 Ligand excluded by PLIP MC3.16: 5 residues within 4Å: Chain B: V.15, R.24, T.28, I.32 Ligands: MC3.15 Ligand excluded by PLIP MC3.17: 5 residues within 4Å: Chain B: P.72, I.73, Y.78, F.81 Ligands: MC3.18 Ligand excluded by PLIP MC3.18: 7 residues within 4Å: Chain B: Y.78, G.212, G.216, L.220 Ligands: MC3.17, MC3.19, MC3.20 Ligand excluded by PLIP MC3.19: 3 residues within 4Å: Chain B: G.212, F.219 Ligands: MC3.18 Ligand excluded by PLIP MC3.20: 2 residues within 4Å: Ligands: MC3.18, MC3.25 Ligand excluded by PLIP MC3.21: 4 residues within 4Å: Chain B: T.88, Y.96, F.198, I.201 Ligand excluded by PLIP MC3.22: 6 residues within 4Å: Chain B: C.92, T.95, F.198 Chain C: M.21, I.25, T.28 Ligand excluded by PLIP MC3.23: 8 residues within 4Å: Chain C: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.24, MC3.25 Ligand excluded by PLIP MC3.24: 5 residues within 4Å: Chain C: F.223, S.224, A.259 Ligands: MC3.23, MC3.25 Ligand excluded by PLIP MC3.25: 4 residues within 4Å: Chain C: V.255 Ligands: MC3.20, MC3.23, MC3.24 Ligand excluded by PLIP MC3.26: 4 residues within 4Å: Chain B: L.10 Chain C: E.8, E.12 Ligands: MC3.27 Ligand excluded by PLIP MC3.27: 6 residues within 4Å: Chain B: V.98 Chain C: V.15, R.24, T.28, V.31 Ligands: MC3.26 Ligand excluded by PLIP MC3.28: 5 residues within 4Å: Chain C: P.72, I.73, Y.78, F.81 Ligands: MC3.29 Ligand excluded by PLIP MC3.29: 6 residues within 4Å: Chain C: G.212, G.216, L.220 Ligands: MC3.28, MC3.30, MC3.31 Ligand excluded by PLIP MC3.30: 2 residues within 4Å: Chain C: G.212 Ligands: MC3.29 Ligand excluded by PLIP MC3.31: 2 residues within 4Å: Ligands: MC3.29, MC3.36 Ligand excluded by PLIP MC3.32: 3 residues within 4Å: Chain C: T.88, F.198, I.201 Ligand excluded by PLIP MC3.33: 6 residues within 4Å: Chain C: C.92, T.95, F.198 Chain D: M.21, I.25, T.28 Ligand excluded by PLIP MC3.34: 8 residues within 4Å: Chain D: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.35, MC3.36 Ligand excluded by PLIP MC3.35: 4 residues within 4Å: Chain D: F.223, S.224 Ligands: MC3.34, MC3.36 Ligand excluded by PLIP MC3.36: 4 residues within 4Å: Chain D: V.255 Ligands: MC3.31, MC3.34, MC3.35 Ligand excluded by PLIP MC3.37: 3 residues within 4Å: Chain C: L.10 Chain D: E.8 Ligands: MC3.38 Ligand excluded by PLIP MC3.38: 6 residues within 4Å: Chain C: V.98 Chain D: V.15, R.24, T.28, V.31 Ligands: MC3.37 Ligand excluded by PLIP MC3.39: 5 residues within 4Å: Chain D: P.72, I.73, Y.78, F.81 Ligands: MC3.40 Ligand excluded by PLIP MC3.40: 6 residues within 4Å: Chain D: G.212, G.216, L.220 Ligands: MC3.39, MC3.41, MC3.42 Ligand excluded by PLIP MC3.41: 3 residues within 4Å: Chain D: G.212, F.219 Ligands: MC3.40 Ligand excluded by PLIP MC3.42: 1 residues within 4Å: Ligands: MC3.40 Ligand excluded by PLIP MC3.43: 4 residues within 4Å: Chain D: T.88, Y.96, F.198, I.201 Ligand excluded by PLIP MC3.44: 6 residues within 4Å: Chain D: C.92, T.95, F.198 Chain E: M.21, I.25, T.28 Ligand excluded by PLIP MC3.45: 8 residues within 4Å: Chain E: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.46, MC3.47 Ligand excluded by PLIP MC3.46: 5 residues within 4Å: Chain E: F.223, S.224, A.259 Ligands: MC3.45, MC3.47 Ligand excluded by PLIP MC3.47: 3 residues within 4Å: Chain E: V.255 Ligands: MC3.45, MC3.46 Ligand excluded by PLIP MC3.48: 4 residues within 4Å: Chain D: L.10 Chain E: E.8, E.12 Ligands: MC3.49 Ligand excluded by PLIP MC3.49: 6 residues within 4Å: Chain D: V.98 Chain E: V.15, R.24, T.28, I.32 Ligands: MC3.48 Ligand excluded by PLIP MC3.50: 5 residues within 4Å: Chain E: P.72, I.73, Y.78, F.81 Ligands: MC3.51 Ligand excluded by PLIP MC3.51: 7 residues within 4Å: Chain E: Y.78, G.212, G.216, L.220 Ligands: MC3.50, MC3.52, MC3.53 Ligand excluded by PLIP MC3.52: 3 residues within 4Å: Chain E: G.212, F.219 Ligands: MC3.51 Ligand excluded by PLIP MC3.53: 2 residues within 4Å: Ligands: MC3.51, MC3.64 Ligand excluded by PLIP MC3.54: 3 residues within 4Å: Chain E: T.88, F.198, I.201 Ligand excluded by PLIP MC3.55: 6 residues within 4Å: Chain E: C.92, T.95, F.198 Chain F: M.21, I.25, T.28 Ligand excluded by PLIP MC3.56: 5 residues within 4Å: Chain F: P.72, I.73, Y.78, F.81 Ligands: MC3.57 Ligand excluded by PLIP MC3.57: 6 residues within 4Å: Chain F: G.212, G.216, L.220 Ligands: MC3.56, MC3.58, MC3.59 Ligand excluded by PLIP MC3.58: 2 residues within 4Å: Chain F: G.212 Ligands: MC3.57 Ligand excluded by PLIP MC3.59: 2 residues within 4Å: Ligands: MC3.3, MC3.57 Ligand excluded by PLIP MC3.60: 3 residues within 4Å: Chain F: T.88, F.198, I.201 Ligand excluded by PLIP MC3.61: 6 residues within 4Å: Chain A: M.21, I.25, T.28 Chain F: C.92, T.95, F.198 Ligand excluded by PLIP MC3.62: 8 residues within 4Å: Chain F: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.63, MC3.64 Ligand excluded by PLIP MC3.63: 5 residues within 4Å: Chain F: F.223, S.224, A.259 Ligands: MC3.62, MC3.64 Ligand excluded by PLIP MC3.64: 4 residues within 4Å: Chain F: V.255 Ligands: MC3.53, MC3.62, MC3.63 Ligand excluded by PLIP MC3.65: 4 residues within 4Å: Chain E: L.10 Chain F: E.8, E.12 Ligands: MC3.66 Ligand excluded by PLIP MC3.66: 7 residues within 4Å: Chain E: V.98 Chain F: V.15, R.24, T.28, V.31, I.32 Ligands: MC3.65 Ligand excluded by PLIP MC3.67: 6 residues within 4Å: Chain G: F.223, S.224, T.251, V.255, F.258 Ligands: MC3.68 Ligand excluded by PLIP MC3.68: 5 residues within 4Å: Chain G: V.252, V.255, F.256 Ligands: MC3.67, MC3.76 Ligand excluded by PLIP MC3.69: 1 residues within 4Å: Ligands: MC3.79 Ligand excluded by PLIP MC3.70: 5 residues within 4Å: Chain G: G.194, R.197, F.198, I.201, F.205 Ligand excluded by PLIP MC3.71: 7 residues within 4Å: Chain G: P.72, I.73, Y.78, F.81 Ligands: MC3.72, MC3.74, MC3.108 Ligand excluded by PLIP MC3.72: 7 residues within 4Å: Chain G: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.71, MC3.73 Ligand excluded by PLIP MC3.73: 3 residues within 4Å: Chain G: G.212, F.219 Ligands: MC3.72 Ligand excluded by PLIP MC3.74: 3 residues within 4Å: Ligands: MC3.71, MC3.108, MC3.109 Ligand excluded by PLIP MC3.75: 4 residues within 4Å: Chain G: I.22 Chain H: F.198, I.201, F.205 Ligand excluded by PLIP MC3.76: 7 residues within 4Å: Chain H: P.72, I.73, Y.78, F.81 Ligands: MC3.68, MC3.77, MC3.79 Ligand excluded by PLIP MC3.77: 8 residues within 4Å: Chain H: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.76, MC3.78, MC3.79 Ligand excluded by PLIP MC3.78: 3 residues within 4Å: Chain H: G.212, F.219 Ligands: MC3.77 Ligand excluded by PLIP MC3.79: 3 residues within 4Å: Ligands: MC3.69, MC3.76, MC3.77 Ligand excluded by PLIP MC3.80: 6 residues within 4Å: Chain H: F.223, S.224, T.251, V.255, F.258 Ligands: MC3.81 Ligand excluded by PLIP MC3.81: 5 residues within 4Å: Chain H: V.252, V.255, F.256 Ligands: MC3.80, MC3.87 Ligand excluded by PLIP MC3.82: 1 residues within 4Å: Ligands: MC3.90 Ligand excluded by PLIP MC3.83: 6 residues within 4Å: Chain I: F.223, S.224, T.251, V.255, F.258 Ligands: MC3.84 Ligand excluded by PLIP MC3.84: 5 residues within 4Å: Chain I: V.252, V.255, F.256 Ligands: MC3.83, MC3.95 Ligand excluded by PLIP MC3.85: 1 residues within 4Å: Ligands: MC3.98 Ligand excluded by PLIP MC3.86: 5 residues within 4Å: Chain H: I.22 Chain I: G.194, F.198, I.201, F.205 Ligand excluded by PLIP MC3.87: 7 residues within 4Å: Chain I: P.72, I.73, Y.78, F.81 Ligands: MC3.81, MC3.88, MC3.90 Ligand excluded by PLIP MC3.88: 8 residues within 4Å: Chain I: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.87, MC3.89, MC3.90 Ligand excluded by PLIP MC3.89: 3 residues within 4Å: Chain I: G.212, F.219 Ligands: MC3.88 Ligand excluded by PLIP MC3.90: 3 residues within 4Å: Ligands: MC3.82, MC3.87, MC3.88 Ligand excluded by PLIP MC3.91: 6 residues within 4Å: Chain J: F.223, S.224, T.251, V.255, F.258 Ligands: MC3.92 Ligand excluded by PLIP MC3.92: 5 residues within 4Å: Chain J: V.252, V.255, F.256 Ligands: MC3.91, MC3.103 Ligand excluded by PLIP MC3.93: 1 residues within 4Å: Ligands: MC3.106 Ligand excluded by PLIP MC3.94: 5 residues within 4Å: Chain J: G.194, R.197, F.198, I.201, F.205 Ligand excluded by PLIP MC3.95: 7 residues within 4Å: Chain J: P.72, I.73, Y.78, F.81 Ligands: MC3.84, MC3.96, MC3.98 Ligand excluded by PLIP MC3.96: 8 residues within 4Å: Chain J: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.95, MC3.97, MC3.98 Ligand excluded by PLIP MC3.97: 3 residues within 4Å: Chain J: G.212, F.219 Ligands: MC3.96 Ligand excluded by PLIP MC3.98: 3 residues within 4Å: Ligands: MC3.85, MC3.95, MC3.96 Ligand excluded by PLIP MC3.99: 6 residues within 4Å: Chain K: F.223, S.224, T.251, V.255, F.258 Ligands: MC3.100 Ligand excluded by PLIP MC3.100: 5 residues within 4Å: Chain K: V.252, V.255, F.256 Ligands: MC3.99, MC3.111 Ligand excluded by PLIP MC3.101: 1 residues within 4Å: Ligands: MC3.114 Ligand excluded by PLIP MC3.102: 4 residues within 4Å: Chain J: I.22 Chain K: F.198, I.201, F.205 Ligand excluded by PLIP MC3.103: 7 residues within 4Å: Chain K: P.72, I.73, Y.78, F.81 Ligands: MC3.92, MC3.104, MC3.106 Ligand excluded by PLIP MC3.104: 8 residues within 4Å: Chain K: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.103, MC3.105, MC3.106 Ligand excluded by PLIP MC3.105: 3 residues within 4Å: Chain K: G.212, F.219 Ligands: MC3.104 Ligand excluded by PLIP MC3.106: 3 residues within 4Å: Ligands: MC3.93, MC3.103, MC3.104 Ligand excluded by PLIP MC3.107: 6 residues within 4Å: Chain L: F.223, S.224, T.251, V.255, F.258 Ligands: MC3.108 Ligand excluded by PLIP MC3.108: 6 residues within 4Å: Chain L: V.252, V.255, F.256 Ligands: MC3.71, MC3.74, MC3.107 Ligand excluded by PLIP MC3.109: 1 residues within 4Å: Ligands: MC3.74 Ligand excluded by PLIP MC3.110: 5 residues within 4Å: Chain L: G.194, R.197, F.198, I.201, F.205 Ligand excluded by PLIP MC3.111: 7 residues within 4Å: Chain L: P.72, I.73, Y.78, F.81 Ligands: MC3.100, MC3.112, MC3.114 Ligand excluded by PLIP MC3.112: 8 residues within 4Å: Chain L: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.111, MC3.113, MC3.114 Ligand excluded by PLIP MC3.113: 3 residues within 4Å: Chain L: G.212, F.219 Ligands: MC3.112 Ligand excluded by PLIP MC3.114: 3 residues within 4Å: Ligands: MC3.101, MC3.111, MC3.112 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

2023-03-22

Peptides

Gap junction delta-2 protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

G
A

H
B

I
C

J
D

K
E

L
F

Membrane

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

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