SMTL ID : 5gjv.1

Structure of the mammalian voltage-gated calcium channel Cav1.1 complex at near atomic resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain E: N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain E: R.86, N.615 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain E: L.593, F.897, N.898, F.985 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain E: N.678, E.681 No protein-ligand interaction detected (PLIP)

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.3: 6 residues within 4Å: Chain E: R.116, S.121, V.124, N.186, S.189, A.190 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.116, E:R.116 NAG-NAG-BMA.4: 6 residues within 4Å: Chain E: Q.110, W.115, N.470, T.472, K.482, L.487 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG.7: 7 residues within 4Å: Chain E: D.45, T.48, L.49, T.52, I.729, G.731, N.827 No protein-ligand interaction detected (PLIP)

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

NAG.8: 1 residues within 4Å: Chain A: N.257 No protein-ligand interaction detected (PLIP) NAG.25: 1 residues within 4Å: Chain E: N.326 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.326 NAG.26: 1 residues within 4Å: Chain E: N.891 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.891 NAG.27: 3 residues within 4Å: Chain E: N.94, E.201, D.202 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.94, E:E.201 NAG.28: 3 residues within 4Å: Chain E: K.604, G.605, N.606 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.604 Hydrogen bonds: E:N.606 NAG.29: 3 residues within 4Å: Chain E: F.783, N.784, R.876 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain E: N.1001, C.1027 No protein-ligand interaction detected (PLIP) NAG.31: 4 residues within 4Å: Chain E: I.892, S.893, N.988, F.993 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.893

14 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.9: 15 residues within 4Å: Chain A: F.205, I.209, Y.210, I.213, L.217, F.218, G.249, I.305, W.309, I.312, Y.313, I.1230, A.1233, F.1234, L.1237 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.205, A:I.209, A:Y.210, A:I.213, A:I.213, A:L.217, A:W.309, A:W.309, A:I.312, A:Y.313, A:F.1234, A:F.1234, A:L.1237 PC1.10: 13 residues within 4Å: Chain A: E.76, K.162, A.166, F.167, L.170, L.576, L.580, R.584, A.626, Y.627, P.633, L.636, V.637 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.170, A:L.576, A:L.576, A:L.580, A:V.637 Salt bridges: A:E.76, A:R.584, A:R.584 PC1.11: 11 residues within 4Å: Chain A: P.521, L.522, S.525, V.526, F.942, I.945, L.949, R.1038, M.1041, I.1043, F.1044 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.522, A:V.526, A:F.942, A:F.942, A:I.945, A:L.949, A:F.1044, A:F.1044 Hydrogen bonds: A:R.1038 Salt bridges: A:R.1038 PC1.12: 6 residues within 4Å: Chain A: I.895, V.898, L.899, I.1284, M.1288, F.1356 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.895, A:V.898, A:V.898, A:L.899, A:I.1284 PC1.13: 11 residues within 4Å: Chain A: M.193, L.196, A.200, L.328, V.646, N.649, L.653, M.1057, F.1060 Ligands: PC1.14, PC1.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.196, A:A.200, A:V.646, A:F.1060 PC1.14: 3 residues within 4Å: Chain A: I.325 Ligands: PC1.13, PC1.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.325 PC1.15: 8 residues within 4Å: Chain A: N.649, L.652, F.1013, I.1050, A.1053 Ligands: PC1.13, PC1.14, PC1.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.652, A:L.652, A:F.1013, A:I.1050, A:I.1050 PC1.16: 7 residues within 4Å: Chain A: L.319, S.322, F.323, T.1321, L.1375 Ligands: PC1.17, PC1.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.323, A:T.1321, A:L.1375 PC1.17: 6 residues within 4Å: Chain A: I.925, M.1056, Y.1365 Ligands: PC1.15, PC1.16, CA.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.925, A:Y.1365 PC1.18: 9 residues within 4Å: Chain A: D.994, L.1001, S.1002, M.1005, S.1333, Y.1358, Y.1359, S.1363, M.1366 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1001, A:L.1001, A:Y.1358, A:Y.1359 Salt bridges: A:D.994 PC1.19: 12 residues within 4Å: Chain A: L.204, N.277, F.278, G.279, M.282, M.1129, T.1132, G.1136, H.1139, Y.1140, H.1141 Ligands: PC1.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.204 Hydrogen bonds: A:N.277 Salt bridges: A:H.1139 pi-Cation interactions: A:H.1139 PC1.20: 5 residues within 4Å: Chain A: N.277, G.279, Y.286, V.635 Ligands: PC1.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.635 PC1.21: 4 residues within 4Å: Chain A: F.567, P.601, L.604, I.1046 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.567, A:P.601, A:L.604, A:I.1046 PC1.22: 10 residues within 4Å: Chain A: N.307, E.308, W.311, L.319, I.1274, F.1278, P.1310, Q.1311, V.1313 Ligands: PC1.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.311, A:W.311, A:L.319, A:I.1274, A:F.1278, A:P.1310 Hydrogen bonds: A:N.307, A:Q.1311

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.23: 3 residues within 4Å: Chain A: E.292, E.614, E.1014 No protein-ligand interaction detected (PLIP) CA.24: 1 residues within 4Å: Ligands: PC1.17 No protein-ligand interaction detected (PLIP) CA.32: 5 residues within 4Å: Chain E: S.263, S.265, T.333, D.365, G.366 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, J.P. et al., Structure of the voltage-gated calcium channel Cav1.1 at 3.6 angstrom resolution. Nature (2016)

Release Date

2016-09-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

Membrane

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

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

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

Voltage-dependent calcium channel gamma-1 subunit

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

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