9L38 | pdb_00009l38

Structure of ENBT1 in the apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9L38

This is version 1.1 of the entry. See complete history

Literature

Structures of the neutral amino acid transporter LAT4 provide insights into antitumor effects of its inhibitor tubeimoside-1.

Ding, D.Lu, Y.Yang, J.Chen, H.Jiang, P.Jin, Y.Luo, J.Wang, G.Yin, Y.

(2026) EMBO J 45: 4283-4298

  • DOI: https://doi.org/10.1038/s44318-026-00786-0
  • Primary Citation Related Structures: 
    9JBS, 9JBT, 9JBU, 9L38

  • PubMed Abstract: 

    Methionine restriction has emerged as a promising strategy for extending lifespan and enhancing cancer therapy. LAT4, an amino acid transporter encoded by SLC43A2, is frequently overexpressed in multiple cancers and critically contributes to systemic methionine accumulation. However, the structural basis of LAT4 function remains poorly understood, and no effective inhibitors have been developed to date. In this study, we present high-resolution cryo-electron microscopy structures of LAT4 and the related SLC43A3-encoded purine transporter ENBT1. The phenylalanine-bound structure of LAT4 enables the characterization of the substrate binding pocket. Comparison of the outward-facing ENBT1 and inward-facing LAT4 structures identifies key residues involved in the methionine transport process. Structural analysis of digitonin binding to the central cavity of LAT4 enabled identification of tubeimoside-1 (TBM-1) as a potent inhibitor of LAT4-mediated methionine uptake. We demonstrate that tubeimoside-1 reduces methionine uptake in B16F10 cancer cells. Furthermore, TBM-1 suppresses tumor progression in the MMTV-PyVT mouse model of breast cancer through systemic methionine restriction. Our study provides insights into the LAT4 transport mechanism and identifies tubeimoside-1 as a potent inhibitor of methionine uptake and establishes a foundation for developing LAT4-targeting therapeutics to restrict methionine uptake.


  • Organizational Affiliation
    • Department of Biomedical Sciences, Division of Biomedical Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China.

Macromolecule Content 

  • Total Structure Weight: 54.57 kDa 
  • Atom Count: 3,268 
  • Modeled Residue Count: 412 
  • Deposited Residue Count: 491 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Equilibrative nucleobase transporter 1491Homo sapiensMutation(s): 0 
Gene Names: SLC43A3ENBT1PSEC0252
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBI5 (Homo sapiens)
Explore Q8NBI5 
Go to UniProtKB:  Q8NBI5
PHAROS:  Q8NBI5
GTEx:  ENSG00000134802 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBI5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82030081
National Natural Science Foundation of China (NSFC)China81874235
National Natural Science Foundation of China (NSFC)China82173386

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-24
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references