SMTL ID : 7xlq.1

Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the ligand-free (apo) state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain B: E.541, F.868, N.869, F.956 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 11 residues within 4Å: Chain B: Q.82, W.87, E.89, E.156, N.442, T.444, K.450, L.453, K.454, N.455, L.459 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 7 residues within 4Å: Chain B: D.17, L.21, T.24, I.790, S.794, W.795, N.798 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.17

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 6 residues within 4Å: Chain A: V.1494, M.1497, T.1505, Y.1506, A.1509, L.1513 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.1494, A:T.1505, A:Y.1506, A:Y.1506, A:A.1509, A:L.1513, A:L.1513 Y01.7: 12 residues within 4Å: Chain A: T.564, F.566, L.571, L.574, F.1299, F.1303, L.1310, R.1396, E.1398, M.1399, F.1402, V.1405 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.564, A:F.566, A:L.571, A:L.574, A:F.1299, A:F.1299, A:F.1303, A:F.1303, A:L.1310, A:F.1402, A:F.1402 Hydrogen bonds: A:T.564 Salt bridges: A:R.1396 Y01.9: 9 residues within 4Å: Chain A: A.491, A.494, I.495, H.497, H.498, N.499, Q.500, N.1357, I.1358 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.491, A:I.495, A:H.497, A:I.1358 Hydrogen bonds: A:H.498 Salt bridges: A:H.497, A:H.497 Y01.11: 11 residues within 4Å: Chain A: W.328, I.332, I.336, C.1611, A.1615, F.1618, F.1650, L.1653, M.1654, F.1657, L.1717 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.328, A:I.332, A:I.336, A:A.1615, A:F.1618, A:F.1650, A:F.1657, A:F.1657, A:L.1717 Y01.13: 7 residues within 4Å: Chain A: A.1165, I.1168, A.1172, R.1182, V.1185, L.1186, F.1189 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1168, A:A.1172, A:V.1185, A:L.1186, A:F.1189, A:F.1189 Y01.18: 6 residues within 4Å: Chain A: N.294, I.295, M.1496, M.1497, Y.1499 Ligands: R16.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.294, A:I.295, A:Y.1499, A:Y.1499

7 x R16: HEXADECANE(Non-covalent)

R16.5: 3 residues within 4Å: Chain A: V.1493, Y.1506 Ligands: Y01.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1493 R16.6: 4 residues within 4Å: Chain A: G.159, W.160, L.195, F.613 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.160, A:L.195, A:F.613 R16.8: 7 residues within 4Å: Chain A: T.642, P.644, I.647, M.1397, S.1400, I.1401, V.1404 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.647, A:I.1401, A:V.1404 R16.10: 6 residues within 4Å: Chain A: I.1359, W.1360, L.1362, L.1363, Y.1700, V.1704 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1359, A:W.1360, A:W.1360, A:L.1363, A:Y.1700, A:V.1704 R16.14: 7 residues within 4Å: Chain A: G.225, F.229, I.232, V.299, F.303, I.684, L.688 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.229, A:I.232, A:F.303, A:F.303, A:I.684, A:L.688 R16.15: 6 residues within 4Å: Chain A: L.577, W.586, V.593, V.1295, F.1299, F.1413 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.577, A:W.586, A:W.586, A:V.1295, A:F.1299, A:F.1413, A:F.1413 R16.17: 5 residues within 4Å: Chain A: N.294, L.296, F.297, L.300, M.677 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.297, A:L.300, A:L.300

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

3PE.12: 14 residues within 4Å: Chain A: F.235, I.238, F.242, Y.243, K.246, V.270, L.322, W.326, N.327, L.329, Y.330, N.1571, S.1573, F.1574 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.235, A:I.238, A:W.326, A:L.329, A:Y.330 Hydrogen bonds: A:L.322, A:N.1571, A:S.1573 Salt bridges: A:K.246

2 x CA: CALCIUM ION(Non-covalent)

CA.16: 4 residues within 4Å: Chain A: E.309, E.657, E.1372, G.1662 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.309, A:E.1372, A:G.1662 CA.24: 4 residues within 4Å: Chain A: D.116 Chain B: S.235, S.237, T.305 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:S.235, B:S.237, A:D.116

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

NAG.19: 4 residues within 4Å: Chain B: T.561, F.562, R.563, N.578 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.563 NAG.20: 3 residues within 4Å: Chain B: E.54, R.58, N.587 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.587 NAG.21: 3 residues within 4Å: Chain B: N.649, T.651, E.652 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.649, B:E.652 NAG.22: 1 residues within 4Å: Chain B: N.862 No protein-ligand interaction detected (PLIP) NAG.23: 5 residues within 4Å: Chain B: V.81, R.88, N.94, N.158, W.159 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.81 Hydrogen bonds: B:R.88, B:R.88, B:N.94 NAG.25: 2 residues within 4Å: Chain B: N.66, E.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.66, B:E.173, B:E.173 NAG.26: 1 residues within 4Å: Chain B: N.298 No protein-ligand interaction detected (PLIP) NAG.27: 2 residues within 4Å: Chain B: N.320, N.322 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Molecular insights into the gating mechanisms of voltage-gated calcium channel Ca V 2.3. Nat Commun (2023)

Release Date

2023-02-08

Peptides

Voltage-dependent R-type calcium channel subunit alpha-1E: A
Voltage-dependent calcium channel subunit alpha-2/delta-1: B
Voltage-dependent L-type calcium channel subunit beta-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent R-type calcium channel subunit alpha-1E

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

Voltage-dependent L-type calcium channel subunit beta-1

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