SMTL ID : 7yjo.1

Cryo-EM structure of the monomeric atSPT-ORM1 (LCB2a-deltaN5) complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Non-covalent)

PLS.1: 15 residues within 4Å: Chain A: P.84, F.282, S.283, A.284 Chain B: Y.104, G.166, H.191, S.193, E.243, D.272, A.274, H.275, T.304, T.306, K.307 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:S.283, A:A.284, B:Y.104, B:G.166, B:N.170, B:S.193, B:T.306, B:K.307 Hydrophobic interactions: B:H.191 Salt bridges: B:H.191, B:K.307 pi-Stacking: B:H.191

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

Z1T.2: 12 residues within 4Å: Chain B: Y.9, L.14, F.16, Y.51 Chain C: N.17, W.20, Y.30, S.67, F.68, G.73, P.75, W.88 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.20, C:Y.30, C:Y.30, C:F.68, C:P.75, C:W.88, B:Y.9, B:L.14, B:F.16 Hydrogen bonds: C:N.17, C:N.17, C:S.67, C:G.73, B:Y.51

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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