SMTL ID : 8c82.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

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

Z8A.1: 19 residues within 4Å: Chain A: M.75, N.76, W.79, H.89, I.92, Y.100, T.118, G.122, M.126, I.130, P.134, M.147 Chain C: L.69, I.72, I.73, H.76, Y.110, Y.485, L.490 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:L.69, C:I.72, C:I.73, A:W.79, A:I.92, A:I.130, A:P.134 Hydrogen bonds: C:Y.485, A:W.79, A:W.79 Z8A.4: 18 residues within 4Å: Chain E: M.75, N.76, W.79, H.89, I.92, Y.100, T.118, I.121, G.122, M.126, P.134, M.147 Chain G: L.69, I.72, H.76, Y.110, Y.485, L.490 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: E:W.79, E:I.92, E:I.121, E:M.126, E:P.134, G:L.69, G:I.72 Hydrogen bonds: E:N.76, E:W.79, G:Y.485

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

PLP.2: 8 residues within 4Å: Chain B: S.385, A.386 Chain C: G.225, Y.226, D.331, H.334, T.365, K.366 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:K.366 Hydrogen bonds: C:G.225, C:Y.226, B:A.386 Salt bridges: C:K.366 pi-Stacking: C:H.250 PLP.6: 8 residues within 4Å: Chain F: S.385, A.386 Chain G: G.225, Y.226, D.331, H.334, T.365, K.366 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain G Hydrogen bonds: F:A.386, G:G.225, G:Y.226 Hydrophobic interactions: G:K.366 Salt bridges: G:K.366 pi-Stacking: G:H.250

2 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.3: 8 residues within 4Å: Chain A: I.130, K.131, D.143, Q.220 Chain C: F.80, M.83, N.105, F.106 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:K.131, A:D.143, A:D.143, A:Q.220, C:N.105, C:N.105 Hydrophobic interactions: C:F.80 Q7G.5: 11 residues within 4Å: Chain E: I.130, K.131, D.143, N.144, Q.220 Chain G: H.76, F.80, M.83, T.84, K.87, F.106 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain G Hydrogen bonds: E:K.131, E:D.143, E:Q.220, G:K.87, G:N.105 Hydrophobic interactions: G:F.80, G:F.106

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: AE
Serine palmitoyltransferase 1: BF
Serine palmitoyltransferase 2: CG
Serine palmitoyltransferase-regulating protein TSC3: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

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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