SMTL ID : 8hlp.1

Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 (apo)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

9 x R16: HEXADECANE(Non-covalent)

R16.1: 3 residues within 4Å: Chain A: M.1105, M.1106, V.1453 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1453 R16.2: 3 residues within 4Å: Chain A: A.542, H.545, L.1102 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.542, A:L.1102 R16.3: 10 residues within 4Å: Chain A: Y.282, I.285, W.380, I.383, T.387, T.1326, F.1327, L.1330, M.1334 Ligands: R16.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.285, A:W.380, A:I.383, A:T.1326, A:F.1327, A:F.1327, A:L.1330 R16.4: 3 residues within 4Å: Chain A: Y.282, W.1283 Ligands: R16.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.282 R16.5: 7 residues within 4Å: Chain A: N.348, A.350, P.722, F.724, M.727, L.728, I.731 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.724, A:L.728, A:I.731 R16.7: 5 residues within 4Å: Chain A: F.659, F.700, V.1140, I.1144, I.1147 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.659, A:F.700, A:F.700, A:V.1140, A:I.1147 R16.8: 1 residues within 4Å: Chain A: N.158 No protein-ligand interaction detected (PLIP) R16.9: 2 residues within 4Å: Chain A: M.1238, H.1240 No protein-ligand interaction detected (PLIP) R16.10: 1 residues within 4Å: Chain A: L.1246 No protein-ligand interaction detected (PLIP)

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.6: 9 residues within 4Å: Chain A: D.232, A.235, F.239, L.668, L.672, Y.719, P.725, L.728, I.731 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.232, A:A.235, A:F.239, A:F.239, A:L.668, A:L.672, A:Y.719, A:L.728, A:I.731 3PE.11: 14 residues within 4Å: Chain A: L.268, V.275, M.353, F.357, I.360, T.361, M.362, V.396, L.397, I.738, N.741, F.1114, Y.1460 Ligands: CA.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.268, A:V.275, A:F.357, A:F.357, A:V.396, A:I.738 Hydrogen bonds: A:N.741, A:Y.1460, A:Y.1460

2 x CA: CALCIUM ION(Non-covalent)

CA.12: 3 residues within 4Å: Chain A: E.363, E.1115 Ligands: 3PE.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.363 CA.13: 4 residues within 4Å: Chain A: E.363, E.706, E.1115, E.1416 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.363, A:E.1115, A:E.1115

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.14: 8 residues within 4Å: Chain B: Q.108, E.182, N.468, T.470, L.479, K.480, N.481, L.485 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.485 Hydrogen bonds: B:Q.108, B:T.470, B:K.480 NAG.15: 1 residues within 4Å: Chain B: N.324 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain B: K.88, S.91, N.92, K.95 No protein-ligand interaction detected (PLIP) NAG.17: 4 residues within 4Å: Chain B: H.111, R.114, N.184, W.185 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.185 Hydrogen bonds: B:R.114 NAG.18: 5 residues within 4Å: Chain B: L.566, E.567, A.893, F.894, N.895 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.566 Hydrogen bonds: B:N.895

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, Y. et al., Structural bases of inhibitory mechanism of Ca V 1.2 channel inhibitors. Nat Commun (2024)

Release Date

2024-04-24

Peptides

Voltage-dependent L-type calcium channel subunit alpha: A
Voltage-dependent calcium channel subunit alpha-2/delta-1: B
Isoform 2c of Voltage-dependent L-type calcium channel subunit beta-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
C

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent L-type calcium channel subunit alpha

Voltage-dependent calcium channel subunit alpha-2/delta-1

Isoform 2c of Voltage-dependent L-type calcium channel subunit beta-2

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