SMTL ID : 8qog.1

Cryo-EM structure of the yeast SPT-Orm2-Monomer complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x WAR: ~{N}-[(2~{S},3~{S},4~{R})-1,3,4-tris(oxidanyl)octadecan-2-yl]heptacosanamide

WAR.1: 20 residues within 4Å: Chain A: N.71, I.83, H.84, G.116, F.117, M.120, V.124, G.126, P.128, M.141 Chain C: Y.65, I.72, I.73, L.74, H.76, V.77, F.106, Y.110, L.490 Ligands: Q7G.3 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:I.83, C:Y.65, C:I.72, C:I.73, C:L.74, C:H.76, C:V.77, C:L.490 Hydrogen bonds: A:N.71, A:M.120, A:G.126

1 x PLP: PYRIDOXAL-5'-PHOSPHATE

PLP.2: 12 residues within 4Å: Chain B: S.407, A.408 Chain C: M.224, G.225, Y.226, H.250, D.331, A.333, H.334, T.363, T.365, K.366 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.333, C:K.366 Hydrogen bonds: C:G.225, C:Y.226, B:S.407, B:A.408 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

Q7G.3: 9 residues within 4Å: Chain A: V.124, K.125, D.137 Chain C: F.80, T.84, L.94, N.105, F.106 Ligands: WAR.1 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.80, C:F.80, C:F.80, C:F.106 Hydrogen bonds: C:T.84, C:N.105, A:K.125, A:D.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korner, C. et al., The structure of the Orm2-containing serine palmitoyltransferase complex reveals distinct inhibitory potentials of yeast Orm proteins. Cell Rep (2024)

Release Date

2024-09-04

Peptides

ORM2 isoform 1: 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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ORM2 isoform 1

Serine palmitoyltransferase 1

Serine palmitoyltransferase 2

Serine palmitoyltransferase-regulating protein TSC3

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