SMTL ID : 7wli.1

CryoEM structure of human low-voltage activated T-type calcium channel CaV3.3 (apo)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.357, E.821, N.1679 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.357 CA.2: 3 residues within 4Å: Chain A: E.357, Q.820, G.1677 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: N.1345, S.1347, D.1348 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: D.1339, R.1341, N.1342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.1341

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

3PE.5: 13 residues within 4Å: Chain A: L.1299, F.1374, A.1377, S.1378, K.1379, V.1422, M.1425, L.1715, Q.1718, F.1719, I.1722 Ligands: Y01.11, 3PE.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1299, A:V.1422, A:L.1715, A:L.1715, A:Q.1718, A:I.1722 Hydrogen bonds: A:Q.1718 Salt bridges: A:K.1379 3PE.6: 4 residues within 4Å: Chain A: I.1491, F.1495, C.1498, M.1601 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1491, A:F.1495 3PE.7: 2 residues within 4Å: Chain A: F.217, A.1602 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.217 3PE.8: 4 residues within 4Å: Chain A: L.1323, N.1404, W.1406 Ligands: 3PE.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1323, A:W.1406 3PE.14: 4 residues within 4Å: Chain A: V.729, T.732, L.735 Ligands: 3PE.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.729, A:V.729, A:T.732, A:L.735 3PE.16: 10 residues within 4Å: Chain A: L.356, I.382, F.387, F.1626, F.1672, S.1675, T.1676, Q.1718, L.1721 Ligands: 3PE.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.356, A:I.382, A:F.387, A:F.1626, A:F.1672, A:T.1676, A:L.1721 3PE.17: 7 residues within 4Å: Chain A: M.759, C.766, F.854, L.1416, I.1417, F.1420, L.1423 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.854, A:L.1416, A:I.1417, A:F.1420, A:F.1420 3PE.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.19: 9 residues within 4Å: Chain A: M.770, L.808, I.811, P.1405, W.1406, L.1408, L.1409, I.1412 Ligands: 3PE.20 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.808, A:L.808, A:I.811, A:P.1405, A:L.1408, A:L.1409, A:L.1409, A:I.1412 3PE.20: 4 residues within 4Å: Chain A: L.807, L.808, I.811 Ligands: 3PE.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.807, A:L.808, A:I.811 3PE.21: 9 residues within 4Å: Chain A: N.342, G.344, Y.345, W.347, I.348, P.836, W.837, S.839, V.843 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.347, A:I.348, A:W.837, A:V.843

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.9: 13 residues within 4Å: Chain A: F.223, I.226, L.230, N.275, H.370, S.371, Y.373, N.374, I.376, Y.377, L.380, V.384, R.1585 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.223, A:F.223, A:I.226, A:I.226, A:Y.373, A:I.376, A:Y.377, A:L.380, A:V.384 Salt bridges: A:H.370, A:R.1585 Y01.10: 6 residues within 4Å: Chain A: V.655, G.658, H.661, N.1365, L.1366 Ligands: Y01.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.655, A:H.661, A:L.1366, A:L.1366, A:L.1366 Salt bridges: A:H.661 Y01.11: 10 residues within 4Å: Chain A: C.1314, N.1365, G.1367, M.1371, F.1374, Q.1703, F.1704, P.1707 Ligands: 3PE.5, Y01.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.1371, A:F.1704, A:P.1707 Y01.12: 7 residues within 4Å: Chain A: L.779, T.834, S.835, W.837, A.838, L.840, Y.841 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.779, A:A.838, A:L.840, A:Y.841 Y01.13: 10 residues within 4Å: Chain A: F.372, F.375, I.379, I.383, M.1627, G.1665, F.1668, L.1669, F.1672 Ligands: Y01.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.372, A:F.375, A:I.383, A:F.1672 Y01.15: 12 residues within 4Å: Chain A: F.1181, C.1184, I.1185, A.1188, L.1189, R.1191, Q.1193, F.1631, N.1663, F.1664, G.1665 Ligands: Y01.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1185, A:F.1631, A:F.1631, A:N.1663, A:F.1664 Salt bridges: A:R.1191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, L. et al., Structure, gating, and pharmacology of human Ca V 3.3 channel. Nat Commun (2022)

Release Date

2022-05-04

Peptides

Voltage-dependent T-type calcium channel subunit alpha-1I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

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

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