SMTL ID : 8eog.1

Structure of the human L-type voltage-gated calcium channel Cav1.2 complexed with L-leucine

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 8 residues within 4Å: Chain A: Q.82, W.87, E.89, N.442, T.444, K.454, N.455, L.459 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.89

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

NAG-NAG.2: 4 residues within 4Å: Chain A: A.867, F.868, N.869, F.956 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: D.17, T.20, L.21, N.798 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.20

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.4: 2 residues within 4Å: Chain A: N.66, E.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.66, A:E.173 NAG.5: 3 residues within 4Å: Chain A: R.88, N.94, N.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.94, A:N.158 NAG.6: 2 residues within 4Å: Chain A: N.320, N.322 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.649 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.649, A:N.649 NAG.8: 1 residues within 4Å: Chain A: N.862 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.862

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

CA.9: 4 residues within 4Å: Chain A: S.235, S.237, T.305 Chain B: D.40 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.237, A:T.305 CA.17: 4 residues within 4Å: Chain B: E.252, E.595, E.1004, G.1304 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.1004 CA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 1 residues within 4Å: Chain A: W.420 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.420

1 x LEU: LEUCINE(Non-covalent)

LEU.11: 8 residues within 4Å: Chain A: W.179, Y.210, R.215, W.217, Y.424, D.426, A.427, D.465 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:W.179 Hydrogen bonds: A:Y.424, A:Y.424, A:D.426, A:A.427 Salt bridges: A:R.215

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.12: 5 residues within 4Å: Chain B: N.237, F.238, I.1123, M.1127, H.1129 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.238, B:F.238 CLR.13: 5 residues within 4Å: Chain B: A.431, H.434, N.436, N.989, L.991 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.991 CLR.14: 2 residues within 4Å: Chain B: L.1135, F.1136 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.1135, B:F.1136

1 x WNZ: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl dodecanoate(Non-covalent)

WNZ.15: 5 residues within 4Å: Chain B: A.124, F.128, Y.608, P.614, Y.621 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.124, B:F.128, B:Y.621

1 x WO9: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl heptadecanoate(Non-covalent)

WO9.16: 9 residues within 4Å: Chain B: A.161, V.164, F.246, T.250, M.251, V.285, L.288, I.627, N.630 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.161, B:V.164, B:F.246, B:F.246, B:L.288, B:I.627

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., EMC chaperone-Ca V structure reveals an ion channel assembly intermediate. Nature (2023)

Release Date

2023-05-24

Peptides

Voltage-dependent calcium channel subunit alpha-2/delta-1: A
Isoform 20 of Voltage-dependent L-type calcium channel subunit alpha-1C: B
Voltage-dependent L-type calcium channel subunit beta-3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
K

C
C

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent calcium channel subunit alpha-2/delta-1

Isoform 20 of Voltage-dependent L-type calcium channel subunit alpha-1C

Voltage-dependent L-type calcium channel subunit beta-3