8T60

CryoEM structure of an inward-facing MelBSt at a Na(+)-bound and sugar low-affinity conformation

This is a non-PDB format compatible entry.

Summary for 8T60

• Entry DOI: 10.2210/pdb8t60/pdb
• EMDB information: 41062
• Descriptor: Melibiose permease, Nb725_4, NabFab_H Chain, ... (5 entities in total)
• Functional Keywords: sugar transporter; cation-coupled symporter; na(+) binding; protein conformation; nanobodies; nabfab; cryoem, membrane proteins; protein-protein interaction, transport protein
• Biological source: Salmonella enterica subsp. enterica serovar Typhimurium; More
• Total number of polymer chains: 4
• Total formula weight: 117888.18

Authors

Guan, L. (deposition date: 2023-06-14, release date: 2024-02-28, Last modification date: 2024-11-13)

Primary citation

Hariharan, P.,Shi, Y.,Katsube, S.,Willibal, K.,Burrows, N.D.,Mitchell, P.,Bakhtiiari, A.,Stanfield, S.,Pardon, E.,Kaback, H.R.,Liang, R.,Steyaert, J.,Viner, R.,Guan, L.
Mobile barrier mechanisms for Na + -coupled symport in an MFS sugar transporter.
Elife, 12:-, 2024

PubMed Abstract: While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na-bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.

PubMed: 38381130
DOI: 10.7554/eLife.92462

Experimental method

ELECTRON MICROSCOPY (3.29 Å)