SMTL ID : 9gvk.1

Cryo-EM structure of endogenous ATP-bound LolCDE with LolD-E171Q mutations in nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain C: S.49, Q.94 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain D: S.49, Q.94, D.170 Ligands: ATP.3 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)(Non-covalent)

ATP.2: 23 residues within 4Å: Chain A: R.397 Chain C: Y.15, V.24, S.43, S.44, G.45, S.46, G.47, K.48, S.49, T.50, Q.94, H.204 Chain D: R.138, H.141, E.145, L.146, S.147, G.148, G.149, E.150, N.175 Ligands: MG.1 21 PLIP interactions: 13 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:G.45, C:G.45, C:S.46, C:G.47, C:K.48, C:S.49, C:S.49, C:T.50, C:Q.94, D:R.138, D:H.141, D:S.147, D:S.147, D:G.148, D:E.150, D:E.150, D:N.175 Salt bridges: C:K.48, C:K.48, C:H.204 pi-Stacking: C:Y.15 ATP.3: 22 residues within 4Å: Chain B: Q.414 Chain C: R.138, H.141, E.145, L.146, S.147, G.148, G.149, E.150, N.175 Chain D: Y.15, V.24, S.44, G.45, S.46, G.47, K.48, S.49, T.50, Q.94, H.204 Ligands: MG.4 21 PLIP interactions: 13 interactions with chain D, 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:G.45, D:G.45, D:G.47, D:K.48, D:S.49, D:S.49, D:T.50, D:T.50, D:Q.94, C:R.138, C:S.147, C:S.147, C:G.148, C:G.149, C:E.150, C:N.175, B:Q.414 Salt bridges: D:K.48, D:K.48, D:H.204 pi-Stacking: D:Y.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, W. et al., Deciphering the molecular basis of lipoprotein recognition and transport by LolCDE. Signal Transduct Target Ther (2024)

Release Date

2025-01-08

Peptides

Lipoprotein-releasing system transmembrane protein LolC: A
Lipoprotein-releasing system transmembrane protein LolE: B
Lipoprotein-releasing system ATP-binding protein LolD: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
D

D
F

Membrane

We predict this structure to be a membrane protein.
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Lipoprotein-releasing system transmembrane protein LolC

Lipoprotein-releasing system transmembrane protein LolE

Lipoprotein-releasing system ATP-binding protein LolD

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