SMTL ID : 8iaj.1

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3A) 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: 12 residues within 4Å: Chain A: F.360, S.361, A.362 Chain B: G.225, H.250, E.302, D.331, A.333, H.334, T.363, T.365, K.366 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.333 Hydrogen bonds: B:G.225, B:N.229, B:T.365, A:A.362 Salt bridges: B:K.366 pi-Stacking: B:H.250 PLP.3: 12 residues within 4Å: Chain E: F.360, S.361, A.362 Chain F: G.225, H.250, E.302, D.331, A.333, H.334, T.363, T.365, K.366 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:A.333 Hydrogen bonds: F:G.225, F:N.229, 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: 19 residues within 4Å: Chain B: Y.65, L.69, I.72, H.76, V.77, Y.110, Y.485, L.490 Chain C: N.71, W.74, I.83, H.84, V.87, F.117, I.119, M.120, V.124, P.128, M.141 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:Y.65, B:L.69, B:I.72, B:H.76, B:V.77, B:L.490, C:W.74, C:I.83, C:V.87, C:F.117, C:I.119, C:V.124 Hydrogen bonds: C:N.71, C:M.120 Z1T.4: 19 residues within 4Å: Chain F: Y.65, L.69, I.72, H.76, V.77, Y.110, Y.485, L.490 Chain G: N.71, W.74, I.83, H.84, V.87, F.117, I.119, M.120, V.124, P.128, M.141 14 PLIP interactions: 6 interactions with chain F, 8 interactions with chain G Hydrophobic interactions: F:Y.65, F:L.69, F:I.72, F:H.76, F:V.77, F:L.490, G:W.74, G:I.83, G:V.87, G:F.117, G:I.119, G:V.124 Hydrogen bonds: G:N.71, 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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