SMTL ID : 8qtr.1

Cryo-EM structure of the FB-bound 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: 18 residues within 4Å: Chain A: Y.21, Y.24, F.25, V.40, A.41, I.42, Y.52, Y.65, F.68, F.69, L.72, F.107, Y.108, V.111, F.115, F.144, I.148, G.152 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.25, A:V.40, A:Y.65, A:F.68, A:F.68, A:F.69, A:F.69, A:F.107, A:Y.108, A:V.111, A:F.115, A:F.115, A:I.148 Hydrogen bonds: A:I.42, A:Y.52 3PE.5: 15 residues within 4Å: Chain B: V.37, A.38, V.39, Y.49, Y.62, F.66, L.69, F.104, Y.105, V.108, F.112, F.141, V.145, F.146, G.149 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.38, B:Y.62, B:F.66, B:L.69, B:F.104, B:F.104, B:Y.105, B:Y.105, B:V.108, B:F.112, B:V.145, B:F.146 Hydrogen bonds: B:V.39, B:Y.49, B:Y.49 3PE.7: 20 residues within 4Å: Chain B: K.51, G.52, L.56, C.57, F.60, F.137, A.151, A.155, L.183, L.184, W.187, Y.190, V.191, Q.269 Chain C: S.12, L.13, I.16, A.17, E.20, K.23 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:F.60, B:A.155, B:L.183, B:L.184, B:W.187, B:W.187, B:Y.190, B:V.191, C:L.13, C:I.16, C:A.17, C:E.20, C:E.20 Hydrogen bonds: B:Q.269 Salt bridges: C:K.23, C:K.23 3PE.10: 23 residues within 4Å: Chain A: K.54, G.55, I.56, L.59, V.62, I.140, A.154, A.158, A.161, C.162, L.186, W.190, Y.193, V.194, H.196, Q.272 Chain D: V.8, S.12, L.13, I.16, A.17, E.20, K.23 14 PLIP interactions: 4 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:V.8, D:I.16, D:A.17, A:I.56, A:V.62, A:A.154, A:A.161, A:L.186, A:W.190, A:Y.193, A:V.194 Salt bridges: D:K.23 Hydrogen bonds: A:Q.272, A:Q.272

2 x WXE: Macrofusine(Non-covalent)

WXE.2: 17 residues within 4Å: Chain A: L.178, H.181, D.212, L.215, K.219, N.222, Y.223, T.229, P.230, F.233, W.240, R.244, W.297, I.301, I.304, R.307, L.308 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:K.219, A:Y.223, A:T.229, A:F.233, A:F.233, A:W.240, A:W.297, A:W.297, A:W.297, A:I.301, A:I.304, A:I.304, A:L.308 Hydrogen bonds: A:D.212, A:N.222, A:R.244, A:R.244, A:R.307 Salt bridges: A:R.307 WXE.4: 16 residues within 4Å: Chain B: R.92, R.95, H.178, D.209, L.212, K.216, N.219, Y.220, A.226, F.227, F.230, W.237, W.294, I.298, V.301 Ligands: 7PO.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.212, B:N.219, B:Y.220, B:A.226, B:F.230, B:W.237, B:W.294, B:W.294, B:I.298, B:V.301 Hydrogen bonds: B:H.178, B:K.216, B:K.216 Salt bridges: B:R.92, B:R.95, B:K.216, B:K.216

2 x 7PO: hexacosanoic acid(Covalent)

7PO.3: 25 residues within 4Å: Chain A: H.181, V.184, T.185, L.188, I.189, S.191, S.192, F.195, M.200, G.201, I.204, Y.205, M.208, R.244, L.267, F.269, Y.274, C.276, I.278, S.279, I.282, V.283, L.286, L.290 Ligands: PIJ.11 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.184, A:T.185, A:L.188, A:I.189, A:F.195, A:F.195, A:I.204, A:I.204, A:Y.205, A:Y.205, A:L.267, A:F.269, A:I.278, A:L.286, A:L.290, A:L.290 Hydrogen bonds: A:R.244, A:R.244 7PO.6: 24 residues within 4Å: Chain B: H.178, T.182, L.185, I.186, S.188, S.189, F.192, M.197, G.198, I.201, Y.202, M.205, R.241, F.266, Y.271, I.275, S.276, I.279, V.280, L.283, W.294 Chain C: F.22 Ligands: WXE.4, PIJ.8 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.185, B:L.185, B:I.186, B:F.192, B:F.192, B:I.201, B:I.201, B:Y.202, B:Y.202, B:M.205, B:F.266, B:F.266, B:Y.271, B:I.275, B:I.279, B:V.280, B:L.283, B:L.283, C:F.22, C:F.22 Hydrogen bonds: B:R.241, B:R.241

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.8: 20 residues within 4Å: Chain B: L.184, W.187, S.188, F.192, L.264, F.266, I.275, L.283 Chain C: A.18, V.19, F.22, W.32, F.33, H.34, G.54, I.98, E.100, K.102 Ligands: 7PO.6, NH4.9 18 PLIP interactions: 6 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:L.184, B:W.187, B:F.192, B:F.266, B:I.275, B:L.283, C:A.18, C:V.19, C:F.22, C:F.22, C:W.32 Hydrogen bonds: C:G.54, C:S.56, C:S.56, C:I.98, C:K.102, C:K.102 Salt bridges: C:H.34 PIJ.11: 15 residues within 4Å: Chain A: W.190, F.195, L.267, I.278, L.286 Chain D: V.19, F.22, W.32, F.33, H.34, G.54, I.98, E.100, K.102 Ligands: 7PO.3 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:V.19, D:F.22, D:W.32, D:W.32, A:W.190, A:F.195, A:F.195, A:L.286 Hydrogen bonds: D:K.102, D:K.102 Salt bridges: D:H.34

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

NH4.9: 3 residues within 4Å: Chain C: W.32, T.36 Ligands: PIJ.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.32 NH4.12: 1 residues within 4Å: Chain D: W.32 No protein-ligand interaction detected (PLIP)

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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