9WML

Structural mechanism of substrate binding of the human Proline Transporter

Summary for 9WML

• Entry DOI: 10.2210/pdb9wml/pdb
• EMDB information: 66096
• Descriptor: Sodium-dependent proline transporter, SODIUM ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: transport protein, l-proline
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 73290.20

Authors

Zhou, Y.,Wu, J.X.,Wang, J.Q.,Wang, N.Q. (deposition date: 2025-09-03, release date: 2026-03-25, Last modification date: 2026-09-09)

Primary citation

Zhou, Y.,Wang, N.,Wang, J.,Meng, X.,Wu, J.X.
Structural basis for the transport mechanism and cholesterol modulation of the human proline transporter.
Nat Commun, 17:-, 2026

PubMed Abstract: L-proline, an amino acid, acts as a potent neuromodulator in the central nervous system, with its synaptic concentrations finely regulated by the high-affinity L-proline transporter (PROT). Dysregulation of PROT function is implicated in neuropsychiatric disorders, yet its regulatory mechanisms remain poorly characterized. Here, we present high-resolution cryo-electron microscopy structures of human PROT in L-proline-free consensus and L-proline-bound states. The L-proline-bound structure reveals an occluded conformation, detailing the coordination of substrate and ions. Strikingly, our L-proline-free consensus structures capture an inward-open conformation with a cholesterol molecule bound directly within the substrate-binding site. Transport kinetics studies demonstrate that partial cholesterol depletion increases PROT's apparent affinity for L-proline, confirming that cholesterol inhibits L-proline uptake. Furthermore, we identify a conformationally sensitive site (CHOL1') present only in the inward-open conformation. This work elucidates PROT's transport cycle and demonstrates how cholesterol directly modulates neurotransmitter uptake, offering potential therapeutic strategies for brain disorders.

PubMed: 42091899
DOI: 10.1038/s41467-026-72780-3

Experimental method

ELECTRON MICROSCOPY (2.79 Å)