SMTL ID : 8iam.1

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3D) complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

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

PLP.1: 13 residues within 4Å: Chain A: S.361, A.362 Chain B: Y.226, N.229, H.250, S.252, E.302, D.331, A.333, H.334, T.363, T.365, K.366 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:A.362, B:G.225, B:Y.226, B:N.229, B:S.252, B:T.365, B:T.365 Hydrophobic interactions: B:A.333, B:K.366 Salt bridges: B:K.366 pi-Stacking: B:H.250 PLP.3: 13 residues within 4Å: Chain E: S.361, A.362 Chain F: Y.226, N.229, H.250, S.252, E.302, D.331, A.333, H.334, T.363, T.365, K.366 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:A.333, F:K.366 Hydrogen bonds: F:G.225, F:Y.226, F:N.229, F:S.252, F:T.365, F:T.365, E:A.362 Salt bridges: F:K.366 pi-Stacking: F:H.250

2 x Z1T: N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide(Non-covalent)

Z1T.2: 18 residues within 4Å: Chain B: Y.65, I.72, I.73, H.76, Y.110, Y.485, L.490 Chain C: N.71, W.74, H.84, V.87, L.91, T.112, I.119, M.120, V.124, P.128, M.141 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.74, C:W.74, C:V.87, C:L.91, C:T.112, C:I.119, C:V.124, B:I.72, B:I.73, B:L.490 Hydrogen bonds: C:M.120 Z1T.4: 18 residues within 4Å: Chain F: Y.65, I.72, I.73, H.76, Y.110, Y.485, L.490 Chain G: N.71, W.74, H.84, V.87, L.91, T.112, I.119, M.120, V.124, P.128, M.141 11 PLIP interactions: 3 interactions with chain F, 8 interactions with chain G Hydrophobic interactions: F:I.72, F:I.73, F:L.490, G:W.74, G:W.74, G:V.87, G:L.91, G:T.112, G:I.119, G:V.124 Hydrogen bonds: G:M.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, T. et al., Collaborative regulation of yeast SPT-Orm2 complex by phosphorylation and ceramide. Cell Rep (2024)

Release Date

2024-02-14

Peptides

Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1: AE
Serine palmitoyltransferase 2: BF
Protein ORM2: CG
Serine palmitoyltransferase-regulating protein TSC3: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
D

G
H

D
C

H
G

Membrane

We predict this structure to be a membrane protein.
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Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1

Serine palmitoyltransferase 2

Protein ORM2

Serine palmitoyltransferase-regulating protein TSC3

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