SMTL ID : 7yjk.1

Cryo-EM structure of the dimeric atSPT-ORM1 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: 11 residues within 4Å: Chain A: S.345, A.346 Chain B: G.170, Y.171, H.195, D.276, A.278, H.279, T.308, T.310, K.311 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:A.346, B:G.170, B:Y.171, B:T.310 Hydrophobic interactions: B:H.195, B:A.278, B:K.311 pi-Stacking: B:H.195 PLP.3: 11 residues within 4Å: Chain E: S.345, A.346 Chain F: G.170, Y.171, H.195, D.276, A.278, H.279, T.308, T.310, K.311 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:H.195, F:A.278, F:K.311 Hydrogen bonds: F:G.170, F:Y.171, F:S.197, F:T.310, E:A.346 pi-Stacking: F:H.195

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

Z1T.2: 12 residues within 4Å: Chain B: G.17, F.20, Y.55 Chain C: N.17, W.20, Y.30, I.33, S.67, F.68, G.73, P.75, W.88 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain C Hydrophobic interactions: B:F.20, B:Y.55, C:W.20, C:Y.30, C:Y.30, C:I.33, C:I.33, C:F.68, C:W.88 Hydrogen bonds: B:Y.55, C:N.17, C:N.17, C:S.67, C:G.73 Z1T.4: 12 residues within 4Å: Chain F: G.17, F.20, Y.55 Chain G: N.17, W.20, Y.30, I.33, S.67, F.68, G.73, P.75, W.88 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain F Hydrophobic interactions: G:W.20, G:Y.30, G:Y.30, G:I.33, G:I.33, G:F.68, G:W.88, F:F.20, F:Y.55 Hydrogen bonds: G:N.17, G:N.17, G:S.67, G:G.73, F:Y.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, P. et al., Mechanism of sphingolipid homeostasis revealed by structural analysis of Arabidopsis SPT-ORM1 complex. Sci Adv (2023)

Release Date

2023-04-05

Peptides

Long chain base biosynthesis protein 1: AE
Long chain base biosynthesis protein 2a: BF
ORMDL family protein: CG
Transmembrane protein, putative (DUF3317): 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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Long chain base biosynthesis protein 1

Long chain base biosynthesis protein 2a

ORMDL family protein

Transmembrane protein, putative (DUF3317)

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