SMTL ID : 8qtn.1

Cryo-EM structure of the apo yeast Ceramide Synthase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-mer

Ligands

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

3PE.1: 26 residues within 4Å: Chain A: Y.21, Y.24, R.30, H.37, V.40, A.41, I.42, Y.52, F.61, Y.65, F.68, F.69, L.72, F.107, Y.108, V.111, S.112, F.115, F.144, I.148, G.152, Q.153, F.156, W.157, Y.205, D.209 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.21, A:F.61, A:F.61, A:Y.65, A:F.68, A:F.68, A:F.69, A:L.72, A:Y.108, A:Y.108, A:V.111, A:F.115, A:F.156, A:F.156, A:F.156, A:W.157 Hydrogen bonds: A:R.30 Salt bridges: A:R.30 3PE.3: 22 residues within 4Å: Chain B: K.54, G.55, I.56, L.59, C.60, F.63, L.151, A.154, A.158, A.161, C.162, L.186, Y.193, Q.272 Chain C: V.9, C.10, S.13, L.14, I.17, A.18, E.21, K.24 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:I.56, B:L.59, B:L.59, B:L.151, B:A.154, B:A.158, B:A.161, B:L.186, B:L.186, B:Y.193, C:V.9, C:L.14, C:I.17, C:A.18 Hydrogen bonds: B:I.56, B:Q.272 Salt bridges: C:K.24, C:K.24 3PE.4: 23 residues within 4Å: Chain B: Y.21, Y.24, F.25, H.37, V.40, A.41, V.42, Q.45, Y.52, F.61, Y.65, F.68, F.69, F.107, Y.108, V.111, S.112, F.115, F.144, V.148, G.152, Q.153, F.156 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.24, B:F.25, B:V.40, B:V.42, B:F.61, B:Y.65, B:Y.65, B:F.68, B:F.68, B:F.69, B:F.107, B:V.111, B:F.115, B:F.144, B:V.148, B:V.148, B:F.156, B:F.156 Hydrogen bonds: B:Y.24, B:V.42, B:Q.45, B:Q.45 3PE.8: 25 residues within 4Å: Chain A: K.54, G.55, I.56, D.58, L.59, S.60, V.62, F.63, I.140, L.151, A.154, A.158, C.162, L.186, W.190, Y.193, H.196, Q.272 Chain D: C.10, S.13, L.14, I.17, A.18, E.21, K.24 24 PLIP interactions: 15 interactions with chain A, 9 interactions with chain D Hydrophobic interactions: A:I.56, A:D.58, A:L.59, A:L.59, A:L.59, A:V.62, A:V.62, A:F.63, A:L.151, A:A.154, A:L.186, A:W.190, D:L.14, D:L.14, D:I.17, D:I.17, D:A.18, D:E.21, D:E.21 Hydrogen bonds: A:K.54, A:Q.272 Salt bridges: A:H.196, D:K.24, D:K.24

2 x 7PO: hexacosanoic acid(Covalent)

7PO.2: 21 residues within 4Å: Chain A: H.181, T.185, L.188, I.189, S.191, S.192, F.195, F.197, M.200, G.201, I.204, Y.205, M.208, D.209, D.212, R.244, Y.274, S.279, V.283, I.287 Ligands: PIJ.9 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.185, A:I.189, A:F.195, A:F.195, A:F.197, A:F.197, A:I.204, A:I.204, A:Y.205, A:Y.205, A:Y.205, A:M.208, A:Y.274, A:V.283, A:I.287 Hydrogen bonds: A:R.244 7PO.5: 23 residues within 4Å: Chain B: W.157, H.181, T.185, L.188, I.189, S.191, S.192, F.195, F.197, M.200, G.201, I.204, Y.205, M.208, D.209, D.212, R.244, Y.274, S.279, I.282, L.286, I.287 Ligands: PIJ.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.157, B:L.188, B:L.188, B:I.189, B:F.195, B:F.195, B:F.195, B:F.197, B:F.197, B:I.204, B:Y.205, B:Y.205, B:Y.205, B:M.208, B:I.282, B:I.282, B:L.286, B:I.287 Hydrogen bonds: B:R.244

2 x PIJ: [(2S)-1-hexadecanoyloxy-3-[hydroxy-[(2S,3R,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] heptadecanoate(Non-covalent)

PIJ.6: 19 residues within 4Å: Chain B: S.191, F.195, L.267, F.269, I.278 Chain C: Y.22, F.23, G.26, T.27, N.30, W.33, F.34, H.35, G.55, I.99, E.101, K.103 Ligands: 7PO.5, NH4.7 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:F.195, B:F.195, B:F.269, B:I.278, C:Y.22, C:F.23, C:F.23, C:T.27, C:F.34 Hydrogen bonds: B:L.267, C:E.101, C:K.103, C:K.103 Salt bridges: C:H.35 PIJ.9: 21 residues within 4Å: Chain A: F.195, L.267, F.269, I.278 Chain D: A.19, V.20, Y.22, F.23, G.26, T.27, N.30, W.33, F.34, H.35, G.54, G.55, I.99, E.101, K.103 Ligands: 7PO.2, NH4.10 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain D Hydrophobic interactions: A:F.195, A:F.269, D:V.20, D:Y.22, D:F.23, D:F.23, D:F.23, D:F.23, D:T.27, D:N.30, D:W.33, D:W.33 Hydrogen bonds: D:F.34, D:E.101, D:K.103, D:K.103 Salt bridges: D:H.35

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.7: 2 residues within 4Å: Chain C: W.33 Ligands: PIJ.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.33 NH4.10: 2 residues within 4Å: Chain D: W.33 Ligands: PIJ.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schaefer, J. et al., Cryo-EM Structure of the Yeast Ceramide Synthase Complex. To Be Published (2024)

Release Date

2024-10-23

Peptides

Ceramide synthase LAG1: A
Ceramide synthase LAC1: B
Ceramide synthase subunit LIP1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Ceramide synthase LAG1

Ceramide synthase LAC1

Ceramide synthase subunit LIP1

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