SMTL ID : 8qof.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

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

WAR.1: 18 residues within 4Å: Chain E: N.71, W.74, H.84, V.87, G.116, F.117, I.119, M.120, V.124, G.126, P.128, M.141 Chain H: I.72, I.73, H.76, V.77, F.106, Y.110 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain H Hydrophobic interactions: E:V.87, E:I.119, E:P.128, H:I.72, H:I.72, H:I.73, H:V.77 Hydrogen bonds: E:N.71 WAR.2: 17 residues within 4Å: Chain F: N.71, W.74, V.87, G.116, F.117, M.120, V.124, G.126, P.128 Chain G: Y.65, I.72, I.73, H.76, V.77, F.106, Y.110 Ligands: Q7G.4 10 PLIP interactions: 6 interactions with chain F, 4 interactions with chain G Hydrophobic interactions: F:W.74, F:W.74, F:V.87, G:Y.65, G:I.73, G:H.76, G:V.77 Hydrogen bonds: F:N.71, F:M.120, F:G.126

2 x PLP: PYRIDOXAL-5'-PHOSPHATE

PLP.3: 12 residues within 4Å: Chain B: S.407, A.408 Chain G: G.225, Y.226, H.250, E.302, D.331, A.333, H.334, T.363, T.365, K.366 9 PLIP interactions: 8 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: G:H.250, G:A.333, G:K.366 Hydrogen bonds: G:G.225, G:Y.226, G:E.302, B:A.408 Salt bridges: G:K.366 pi-Stacking: G:H.250 PLP.5: 12 residues within 4Å: Chain A: S.407, A.408 Chain H: G.225, Y.226, H.250, E.302, D.331, A.333, H.334, T.363, T.365, K.366 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:H.250, H:K.366 Hydrogen bonds: H:G.225, H:Y.226, H:S.252, A:A.408 pi-Stacking: H: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

Q7G.4: 10 residues within 4Å: Chain F: K.125, D.137 Chain G: H.76, F.80, M.83, T.84, K.87, L.94, F.106 Ligands: WAR.2 8 PLIP interactions: 1 interactions with chain F, 7 interactions with chain G Hydrogen bonds: F:K.125, G:M.83, G:K.87, G:K.87, G:S.104, G:S.104 Hydrophobic interactions: G:F.80, G:F.80 Q7G.6: 10 residues within 4Å: Chain E: R.45, V.124, K.125, D.137 Chain H: H.76, F.80, M.83, K.87, L.94, F.106 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain E Hydrophobic interactions: H:F.80, H:F.80, H:F.80 Hydrogen bonds: H:K.87, E:R.45, E:K.125, E: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

Serine palmitoyltransferase 1: AB
Serine palmitoyltransferase-regulating protein TSC3: CD
ORM2 isoform 1: EF
Serine palmitoyltransferase 2: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

C
D

D
H

E
A

F
E

G
G

H
C

Membrane

We predict this structure to be a membrane protein.
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Serine palmitoyltransferase 1

Serine palmitoyltransferase-regulating protein TSC3

ORM2 isoform 1

Serine palmitoyltransferase 2

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