SMTL ID : 8hma.1

Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 in complex with tetrandrine (TET)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x R16: HEXADECANE(Non-covalent)

R16.1: 4 residues within 4Å: Chain A: L.539, A.542, H.545, N.1100 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.539

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

3PE.2: 8 residues within 4Å: Chain A: R.378, D.379, W.382, P.1403, Q.1404, V.1406, L.1407, F.1410 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.382, A:W.382, A:P.1403, A:V.1406, A:F.1410 Salt bridges: A:R.378 3PE.3: 3 residues within 4Å: Chain A: D.232, A.235, P.725 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.232, A:A.235 3PE.5: 3 residues within 4Å: Chain A: M.362, Y.742 Ligands: 01.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.742

1 x 01: 6,6',7,12-tetramethoxy-2,2'-dimethyl-1beta-3,4-didehydroberbaman

01.4: 19 residues within 4Å: Chain A: M.362, L.397, L.401, T.704, N.741, F.1114, F.1155, M.1158, N.1159, V.1162, A.1413, Y.1460, C.1463, A.1464, I.1467, I.1468, F.1471 Ligands: 3PE.5, CA.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.397, A:L.401, A:V.1162, A:I.1468, A:F.1471, A:F.1471 Hydrogen bonds: A:N.741

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain A: E.363, E.706, E.1115 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.363, A:E.706, A:E.1115, A:E.1115 CA.7: 6 residues within 4Å: Chain A: E.363, F.1114, E.1115, T.1414, G.1415 Ligands: 01.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.363, A:E.1115, A:G.1415

11 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)

NAG.8: 3 residues within 4Å: Chain C: N.92, E.199, D.200 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.92, C:E.199 NAG.9: 4 residues within 4Å: Chain C: R.114, N.120, N.184, A.188 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.188 Hydrogen bonds: C:R.114, C:N.120 NAG.10: 8 residues within 4Å: Chain C: Q.108, E.182, N.468, T.470, L.479, K.480, N.481 Ligands: NAG.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.108, C:T.470 NAG.11: 3 residues within 4Å: Chain C: W.113 Ligands: NAG.10, BMA.12 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain C: N.888 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.888 NAG.14: 6 residues within 4Å: Chain C: E.80, A.83, R.84, P.611, N.613 Ligands: NAG.15 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.83 Hydrogen bonds: C:E.80, C:R.84, C:N.613, C:N.613 NAG.15: 1 residues within 4Å: Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain C: N.324 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.324 NAG.17: 2 residues within 4Å: Chain C: F.780, N.781 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.780 NAG.18: 4 residues within 4Å: Chain C: E.567, A.893, F.894, N.895 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.895 NAG.19: 2 residues within 4Å: Chain C: N.346, N.348 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.348

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.12: 3 residues within 4Å: Chain C: W.113, E.115 Ligands: NAG.11 No protein-ligand interaction detected (PLIP)

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
F

Membrane

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

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

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

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