SMTL ID : 8izd.1

Cryo-EM structure of the C26-CoA-bound Lac1-Lip1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

6 x 6PL: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

6PL.1: 10 residues within 4Å: Chain A: A.115, V.116, F.135, S.186, F.189, F.218, V.222, G.226, Q.227, F.230 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.115, A:V.116, A:F.135, A:F.189, A:F.218, A:V.222, A:Q.227, A:F.230 6PL.3: 12 residues within 4Å: Chain B: L.33, A.36, V.37, Y.39, G.43, N.47, E.49, W.50, F.51, K.86, R.90 Ligands: 6PL.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.33, B:Y.39 Salt bridges: B:K.86, B:R.90 6PL.4: 7 residues within 4Å: Chain A: G.129, L.133, L.261, W.264, Y.267, V.268 Chain B: E.38 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.133, A:L.261, A:W.264, A:Y.267, A:V.268, B:E.38 6PL.5: 9 residues within 4Å: Chain C: A.115, V.116, F.135, S.186, F.189, F.218, V.222, G.226, Q.227 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.115, C:V.116, C:F.135, C:F.189, C:F.218, C:V.222, C:Q.227 6PL.7: 12 residues within 4Å: Chain D: L.33, A.36, V.37, Y.39, G.43, N.47, E.49, W.50, F.51, K.86, R.90 Ligands: 6PL.3 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.33, D:Y.39 Salt bridges: D:K.86, D:R.90 6PL.8: 7 residues within 4Å: Chain C: G.129, L.133, L.261, W.264, Y.267, V.268 Chain D: E.38 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.133, C:L.261, C:W.264, C:Y.267, C:V.268, D:E.38

2 x 9NY: Hexacosanoyl-CoA(Non-covalent)

9NY.2: 27 residues within 4Å: Chain A: W.231, H.255, T.259, L.262, S.265, S.266, F.271, M.274, G.275, I.278, Y.279, M.282, D.286, L.289, K.293, N.296, F.307, R.318, Y.348, I.352, S.353, I.356, V.357, L.360, W.371, I.375, I.382 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.231, A:L.262, A:L.262, A:F.271, A:F.271, A:I.278, A:I.278, A:Y.279, A:Y.279, A:M.282, A:L.289, A:I.352, A:I.356, A:I.356, A:V.357, A:L.360, A:I.375 Hydrogen bonds: A:D.286, A:N.296, A:R.381 Salt bridges: A:K.293 9NY.6: 27 residues within 4Å: Chain C: W.231, H.255, T.259, L.262, S.265, S.266, F.271, M.274, G.275, I.278, Y.279, M.282, D.286, L.289, K.293, N.296, F.307, R.318, Y.348, I.352, S.353, I.356, V.357, L.360, W.371, I.375, I.382 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:W.231, C:L.262, C:L.262, C:F.271, C:F.271, C:I.278, C:I.278, C:Y.279, C:Y.279, C:M.282, C:L.289, C:I.352, C:I.356, C:I.356, C:V.357, C:L.360, C:I.375 Hydrogen bonds: C:D.286, C:N.296, C:R.381 Salt bridges: C:K.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, T. et al., Structure and mechanism of a eukaryotic ceramide synthase complex. Embo J. (2023)

Release Date

2023-12-13

Peptides

Ceramide synthase LAC1: AC
Ceramide synthase subunit LIP1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Ceramide synthase LAC1

Ceramide synthase subunit LIP1