SMTL ID : 8c80.1

Cryo-EM structure of the yeast SPT-Orm1-Monomer complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x ERG: ERGOSTEROL(Non-covalent)

ERG.1: 1 residues within 4Å: Chain A: F.195 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.195, A:F.195 ERG.3: 4 residues within 4Å: Chain A: F.195, V.199 Chain B: T.43 Ligands: ERG.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.195, A:V.199 ERG.4: 7 residues within 4Å: Chain A: T.194, L.202 Chain B: Y.46, L.47, Y.50, F.51 Ligands: ERG.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.47, B:F.51, A:T.194, A:L.202

1 x Z8A: N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide(Non-covalent)

Z8A.2: 17 residues within 4Å: Chain A: N.76, W.79, H.89, M.117, T.118, Y.119, I.121, G.122, M.126, I.130, P.134, M.147 Chain C: Y.65, I.72, H.76, Y.485, L.490 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.79, A:T.118, A:Y.119, A:Y.119, A:I.121, A:P.134

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.5: 11 residues within 4Å: Chain B: S.407, A.408 Chain C: G.225, Y.226, H.250, D.331, A.333, H.334, T.365, K.366, G.372 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:A.408, C:G.225, C:Y.226 Hydrophobic interactions: C:A.333, C:K.366 Salt bridges: C:K.366 pi-Stacking: C:H.250

1 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)

Q7G.6: 6 residues within 4Å: Chain A: I.130, K.131, D.143, Q.220 Chain B: K.249 Chain C: T.84 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.249, A:K.131, A:D.143, A:Q.220 Hydrophobic interactions: A:I.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schafer, J.H. et al., Structure of the ceramide-bound SPOTS complex. Nat Commun (2023)

Release Date

2023-10-11

Peptides

Protein ORM1: A
Serine palmitoyltransferase 1: B
Serine palmitoyltransferase 2: C
Serine palmitoyltransferase-regulating protein TSC3: D

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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Protein ORM1

Serine palmitoyltransferase 1

Serine palmitoyltransferase 2

Serine palmitoyltransferase-regulating protein TSC3

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