SMTL ID : 6xiw.1

Cryo-EM structure of the sodium leak channel NALCN-FAM155A complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.210, D.211, P.241, G.242 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.241 Hydrogen bonds: A:N.210 NAG.2: 6 residues within 4Å: Chain A: P.1049, F.1061, R.1062, N.1064, L.1075, K.1081 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.1049, A:F.1061 Hydrogen bonds: A:N.1064

5 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.3: 10 residues within 4Å: Chain A: D.952, F.953, G.954, F.997, K.998, R.1004, V.1007, R.1008, F.1011, L.1345 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.953, A:F.953, A:F.997, A:F.1011, A:F.1011, A:F.1011, A:L.1345 Salt bridges: A:R.1008 PEV.4: 11 residues within 4Å: Chain A: L.1025, G.1102, L.1106, F.1109, Y.1420, A.1421, M.1425, C.1428, S.1429, V.1432 Ligands: PEV.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1025, A:L.1106, A:F.1109, A:Y.1420, A:V.1432 PEV.5: 8 residues within 4Å: Chain A: L.881, L.884, I.897, V.1000, Q.1002, Y.1333, F.1336, F.1337 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.897, A:V.1000, A:Y.1333, A:F.1336, A:F.1336, A:F.1337 Hydrogen bonds: A:Q.1002 PEV.6: 14 residues within 4Å: Chain A: Y.192, L.195, Q.198, M.199, W.296, R.297, F.300, F.308, K.1230, M.1301, A.1304, C.1305, V.1308, F.1312 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.296, A:W.296, A:F.300, A:F.308, A:V.1308, A:F.1312 Hydrogen bonds: A:C.1305 Salt bridges: A:R.297, A:R.297 PEV.7: 7 residues within 4Å: Chain A: I.399, S.403, Y.405, N.1100, V.1101 Chain B: Y.365 Ligands: PEV.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.399 Hydrogen bonds: A:N.1100, A:V.1101, A:G.1102, B:Y.365

2 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.8: 15 residues within 4Å: Chain A: E.979, S.980, G.981, Q.983, L.984, L.991, L.1345, Y.1349, A.1352, L.1356, N.1419, G.1422, M.1425, Y.1426 Ligands: Y01.11 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.984, A:L.1345, A:Y.1349, A:A.1352, A:L.1356, A:M.1425, A:Y.1426 Hydrogen bonds: A:E.979, A:G.981, A:N.1419 PGV.9: 16 residues within 4Å: Chain A: V.510, T.513, A.514, L.517, P.541, R.542, F.544, M.545, I.1125, P.1130, G.1133, I.1134, H.1137, V.1138, F.1141 Ligands: Y01.10 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.510, A:T.513, A:A.514, A:L.517, A:F.544, A:P.1130, A:I.1134, A:V.1138, A:F.1141, A:F.1141, A:F.1141 Salt bridges: A:R.542, A:R.542

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.10: 9 residues within 4Å: Chain A: I.51, C.54, T.60, H.63, Y.64, T.539, F.540, P.541 Ligands: PGV.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.51, A:Y.64, A:T.539, A:F.540, A:F.540 Salt bridges: A:H.63, A:R.542 Y01.11: 7 residues within 4Å: Chain A: F.960, L.963, I.967, W.971, G.981, L.985 Ligands: PGV.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.960, A:L.963, A:I.967, A:W.971, A:L.985 Y01.12: 3 residues within 4Å: Chain A: P.916, Y.923, I.927 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.923, A:I.927

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kschonsak, M. et al., Structure of the human sodium leak channel NALCN. Nature (2020)

Release Date

2020-07-29

Peptides

Sodium leak channel non-selective protein: A
Transmembrane protein FAM155A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Sodium leak channel non-selective protein

Transmembrane protein FAM155A

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