9KJU | pdb_00009kju

Local refinement of the y+LAT1-4F2hc bound with Arg


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9KJU

This is version 1.0 of the entry. See complete history

Literature

Structural basis for the substrate recognition and transport mechanism of the human y + LAT1-4F2hc transporter complex.

Dai, L.Zeng, Q.Zhang, T.Zhang, Y.Shi, Y.Li, Y.Xu, K.Huang, J.Wang, Z.Zhou, Q.Yan, R.

(2025) Sci Adv 11: eadq0558-eadq0558

  • DOI: https://doi.org/10.1126/sciadv.adq0558
  • Primary Citation Related Structures: 
    8XXI, 8XYJ, 8YLP, 9KH5, 9KJU

  • PubMed Abstract: 

    Heteromeric amino acid transporters (HATs), including y + LAT1-4F2hc complex, are responsible for transporting amino acids across membranes, and mutations in y + LAT1 cause lysinuric protein intolerance (LPI), a hereditary disorder characterized by defective cationic amino acid transport. The relationship between LPI and specific mutations in y + LAT1 has yet to be fully understood. In this study, we characterized the function of y + LAT1-4F2hc complex in mammalian cells and determined the cryo-EM structures of the human y + LAT1-4F2hc complex in two distinct conformations: the apo state in an inward-open conformation and the native substrate-bound state in an outward-open conformation. Structural analysis suggests that Asp 243 in y + LAT1 plays a crucial role in coordination with sodium ion and substrate selectivity. Molecular dynamic (MD) simulations further revealed the different transport mechanism of cationic amino acids and neutral amino acids. These results provide important insights into the mechanisms of the substrate binding and working cycle of HATs.


  • Organizational Affiliation
    • School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.

Macromolecule Content 

  • Total Structure Weight: 129.67 kDa 
  • Atom Count: 7,398 
  • Modeled Residue Count: 935 
  • Deposited Residue Count: 1,174 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Amino acid transporter heavy chain SLC3A2645Homo sapiensMutation(s): 0 
Gene Names: SLC3A2MDU1
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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08195
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P08195-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Y+L amino acid transporter 1529Homo sapiensMutation(s): 0 
Gene Names: SLC7A7
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM01 (Homo sapiens)
Explore Q9UM01 
Go to UniProtKB:  Q9UM01
PHAROS:  Q9UM01
GTEx:  ENSG00000155465 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM01
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ARG
(Subject of Investigation/LOI)

Query on ARG



Download:Ideal Coordinates CCD File
G [auth B]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release