SMTL ID : 9cjl.1

Molecular basis of TMED9 dodecamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

2 x 9ED: [(2R)-2-[(E)-octadec-9-enoyl]oxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] (E)-octadec-9-enoate

9ED.1: 14 residues within 4Å: Chain A: I.217, W.220 Chain B: I.208, T.211, L.212, V.215, A.216, I.217, V.219, W.220 Chain D: I.213 Chain J: L.212 Chain L: S.207, T.211 12 PLIP interactions: 1 interactions with chain D, 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:I.213, B:I.208, B:T.211, B:L.212, B:L.212, B:V.215, B:V.215, B:A.216, B:V.219, B:V.219, A:I.217 Hydrogen bonds: B:W.220 9ED.2: 16 residues within 4Å: Chain D: L.212, V.215, V.219 Chain E: W.220, R.223 Chain H: Q.201, L.204, W.205, I.208, L.212, L.214, V.219, W.220 Chain I: Q.210, I.213, I.217 15 PLIP interactions: 8 interactions with chain H, 3 interactions with chain E, 1 interactions with chain D, 3 interactions with chain I Hydrophobic interactions: H:L.204, H:W.205, H:I.208, H:I.208, H:L.212, H:L.212, H:L.214, H:V.219, D:V.219, I:I.213, I:I.217, I:I.217 Hydrogen bonds: E:W.220, E:W.220 Salt bridges: E:R.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, L. et al., Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway. Sci Adv (2024)

Release Date

2024-10-02

Peptides

Transmembrane emp24 domain-containing protein 9: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Membrane

We predict this structure to be a membrane protein.
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Transmembrane emp24 domain-containing protein 9

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