SMTL ID : 7yjm.1

Cryo-EM structure of the monomeric atSPT-ORM1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

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

PLP.1: 12 residues within 4Å: Chain A: S.283, A.284 Chain B: G.170, Y.171, H.195, S.197, D.276, A.278, H.279, T.308, T.310, K.311 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.195, B:A.278 Hydrogen bonds: B:G.170, B:Y.171, B:S.197, B:K.311, A:A.284 Salt bridges: B:K.311 pi-Stacking: B:H.195

1 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.13, G.17, L.18, F.20, A.21, Y.55, L.435 Chain C: N.17, W.20, T.29, Y.30, I.33, H.60, S.67, F.68, P.75, F.76, W.88 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:W.20, C:W.20, C:T.29, C:Y.30, C:I.33, C:F.68, C:F.76, B:L.18, B:F.20, B:F.20, B:A.21 Hydrogen bonds: C:N.17, C:N.17, C:S.67, C:G.73, B: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

atLCB1: A
Long chain base biosynthesis protein 2a: B
ORMDL family protein: C
atLCB1: D
Transmembrane protein, putative (DUF3317): E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
C

Membrane

We predict this structure to be a membrane protein.
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atLCB1

Long chain base biosynthesis protein 2a

ORMDL family protein

atLCB1

Transmembrane protein, putative (DUF3317)

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