7NDF

Crystal structure of nanobody Nb_MsbA#1 in complex with the nucleotide binding domain of MsbA

Summary for 7NDF

• Entry DOI: 10.2210/pdb7ndf/pdb
• Descriptor: Nb_MsbA 1, Lipid A ABC transporter ATP-binding protein/permease MsbA (3 entities in total)
• Functional Keywords: nucleotide binding domain, abc transporter, nanobody, protein binding
• Biological source: Vicugna pacos; More
• Total number of polymer chains: 4
• Total formula weight: 78926.69

Authors

Meier, G.,Seeger, M. (deposition date: 2021-02-01, release date: 2022-03-02, Last modification date: 2024-10-16)

Primary citation

Galazzo, L.,Meier, G.,Januliene, D.,Parey, K.,De Vecchis, D.,Striednig, B.,Hilbi, H.,Schafer, L.V.,Kuprov, I.,Moeller, A.,Bordignon, E.,Seeger, M.A.
The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells.
Sci Adv, 8:eabn6845-eabn6845, 2022

PubMed Abstract: Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.

PubMed: 36223470
DOI: 10.1126/sciadv.abn6845

Experimental method

X-RAY DIFFRACTION (2.1 Å)