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- PDB-9kh5: Structure of y+LAT1 -

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Basic information

Entry
Database: PDB / ID: 9kh5
TitleStructure of y+LAT1
ComponentsY+L amino acid transporter 1
KeywordsMEMBRANE PROTEIN / amino acid
Function / homology
Function and homology information


basic amino acid transmembrane transport / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / L-arginine transmembrane transporter activity / : / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / amino acid transmembrane transport / L-amino acid transmembrane transporter activity / L-leucine transport / Amino acid transport across the plasma membrane ...basic amino acid transmembrane transport / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / L-arginine transmembrane transporter activity / : / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / amino acid transmembrane transport / L-amino acid transmembrane transporter activity / L-leucine transport / Amino acid transport across the plasma membrane / Basigin interactions / basolateral plasma membrane / plasma membrane
Similarity search - Function
: / Amino acid/polyamine transporter I / Amino acid permease
Similarity search - Domain/homology
Y+L amino acid transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsYan, R.H. / Dai, L. / Zhang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2025
Title: Structural basis for the substrate recognition and transport mechanism of the human yLAT1-4F2hc transporter complex.
Authors: Lu Dai / Qian Zeng / Ting Zhang / Yuanyuan Zhang / Yi Shi / Yaning Li / Kangtai Xu / Jing Huang / Zilong Wang / Qiang Zhou / Renhong Yan /
Abstract: Heteromeric amino acid transporters (HATs), including yLAT1-4F2hc complex, are responsible for transporting amino acids across membranes, and mutations in yLAT1 cause lysinuric protein intolerance ...Heteromeric amino acid transporters (HATs), including yLAT1-4F2hc complex, are responsible for transporting amino acids across membranes, and mutations in yLAT1 cause lysinuric protein intolerance (LPI), a hereditary disorder characterized by defective cationic amino acid transport. The relationship between LPI and specific mutations in yLAT1 has yet to be fully understood. In this study, we characterized the function of yLAT1-4F2hc complex in mammalian cells and determined the cryo-EM structures of the human yLAT1-4F2hc 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 in yLAT1 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.
History
DepositionNov 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Y+L amino acid transporter 1


Theoretical massNumber of molelcules
Total (without water)57,9631
Polymers57,9631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Y+L amino acid transporter 1 / Monocyte amino acid permease 2 / MOP-2 / Solute carrier family 7 member 7 / y(+)L-type amino acid ...Monocyte amino acid permease 2 / MOP-2 / Solute carrier family 7 member 7 / y(+)L-type amino acid transporter 1 / Y+LAT1 / y+LAT-1


Mass: 57963.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC7A7 / Production host: Homo sapiens (human) / References: UniProt: Q9UM01
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of y+LAT1 in an apo conformation / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276483 / Symmetry type: POINT

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