8KDN | pdb_00008kdn

Structure of LAT1-CD98hc in complex with L-Phe, focused on TMD

• PDB DOI: https://doi.org/10.2210/pdb8KDN/pdb
• EM Map EMD-37140: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-08-09 Released: 2025-02-12 
• Deposition Author(s): Lee, Y.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of anticancer drug recognition and amino acid transport by LAT1.

Lee, Y., Jin, C., Ohgaki, R., Xu, M., Ogasawara, S., Warshamanage, R., Yamashita, K., Murshudov, G., Nureki, O., Murata, T., Kanai, Y.

(2025) Nat Commun 16: 1635-1635

• PubMed: 39952931 
• DOI: https://doi.org/10.1038/s41467-025-56903-w
• Primary Citation Related Structures: 
  8KDD, 8KDF, 8KDG, 8KDH, 8KDI, 8KDJ, 8KDN, 8KDO, 8KDP


• PubMed Abstract: 
  

  LAT1 (SLC7A5) transports large neutral amino acids and plays pivotal roles in cancer proliferation, immune response and drug delivery. Despite recent advances in structural understanding of LAT1, how it discriminates substrates and inhibitors including the clinically relevant drugs remains elusive. Here we report six structures of LAT1 across three conformations with bound ligands, elucidating its substrate transport and inhibitory mechanisms. JPH203 (also known as nanvuranlat or KYT-0353), an anticancer drug in clinical trials, traps LAT1 in an outward-facing state with a U-shaped conformer, with its amino-phenylbenzoxazol moiety pushing against transmembrane helix 3 (TM3) and bending TM10. Physiological substrates like ʟ-Phe lack such effects, whereas melphalan poses steric hindrance, explaining its inhibitory activity. The "classical" system L inhibitor BCH induces an occluded state critical for transport, confirming its substrate-like behavior. These findings provide a structural basis for substrate recognition and inhibition of LAT1, guiding future drug design.

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Organizational Affiliation: 
• Department of Structural Biology, Max Planck Institute of Biophysics, 60438, Frankfurt, Germany. [e-mail].
Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan. [e-mail].
Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, 565-0871, Japan.
Graduate School of Science, Chiba University, Chiba, 263-8522, Japan.
Scientific Computing Department, UKRI Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0FA, UK.
Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan. [e-mail].
Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, 565-0871, Japan. [e-mail].
Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka, 565-0871, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 124.28 kDa 
• Atom Count: 3,930 
• Modeled Residue Count: 506 
• Deposited Residue Count: 1,146 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4F2 cell-surface antigen heavy chain	A	631	Homo sapiens	Mutation(s): 0  Gene Names: SLC3A2, MDU1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P08195 (Homo sapiens) Explore P08195  Go to UniProtKB:  P08195
PHAROS:  P08195 GTEx:  ENSG00000168003

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Large neutral amino acids transporter small subunit 1	B	515	Homo sapiens	Mutation(s): 0  Gene Names: SLC7A5, CD98LC, LAT1, MPE16 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q01650 (Homo sapiens) Explore Q01650  Go to UniProtKB:  Q01650
PHAROS:  Q01650 GTEx:  ENSG00000103257

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHE (Subject of Investigation/LOI)	C [auth B]	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Lee, Y.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Data collection, Database references