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- EMDB-62377: Local refinement of the y+LAT1-4F2hc bound with Arg -

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Basic information

Entry
Database: EMDB / ID: EMD-62377
TitleLocal refinement of the y+LAT1-4F2hc bound with Arg
Map data
Sample
  • Complex: Overall structure of the y+LAT1-4F2hc bound with Arg
    • Protein or peptide: Amino acid transporter heavy chain SLC3A2
    • Protein or peptide: Y+L amino acid transporter 1
  • Ligand: ARGININE
  • Ligand: water
Keywordscomplex / membrane protein / amino acid
Function / homology
Function and homology information


basic amino acid transmembrane transport / L-arginine transmembrane transporter activity / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / regulation of arginine metabolic process / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane ...basic amino acid transmembrane transport / L-arginine transmembrane transporter activity / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / regulation of arginine metabolic process / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / aromatic amino acid transmembrane transporter activity / phenylalanine transport / methionine transport / amino acid transmembrane transport / L-leucine transmembrane transporter activity / isoleucine transport / valine transport / L-amino acid transmembrane transporter activity / proline transport / L-leucine transport / thyroid hormone transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / Tryptophan catabolism / exogenous protein binding / anchoring junction / Basigin interactions / amino acid transport / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / calcium ion transport / melanosome / double-stranded RNA binding / virus receptor activity / basolateral plasma membrane / carbohydrate metabolic process / cadherin binding / apical plasma membrane / protein heterodimerization activity / symbiont entry into host cell / lysosomal membrane / synapse / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / : / Amino acid/polyamine transporter I / Amino acid permease / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Amino acid transporter heavy chain SLC3A2 / Y+L amino acid transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsYan RH / Dai L / Zhang YY / Zhang T
Funding support China, 1 items
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 12, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62377.png

Downloads & links

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Map

FileDownload / File: emd_62377.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0306
Minimum - Maximum-0.09232961 - 0.16555285
Average (Standard dev.)-0.00022310477 (±0.003445234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62377_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62377_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Overall structure of the y+LAT1-4F2hc bound with Arg

EntireName: Overall structure of the y+LAT1-4F2hc bound with Arg
Components
  • Complex: Overall structure of the y+LAT1-4F2hc bound with Arg
    • Protein or peptide: Amino acid transporter heavy chain SLC3A2
    • Protein or peptide: Y+L amino acid transporter 1
  • Ligand: ARGININE
  • Ligand: water

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Supramolecule #1: Overall structure of the y+LAT1-4F2hc bound with Arg

SupramoleculeName: Overall structure of the y+LAT1-4F2hc bound with Arg / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Amino acid transporter heavy chain SLC3A2

MacromoleculeName: Amino acid transporter heavy chain SLC3A2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.837523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHHHHH SGRELQPPEA SIAVVSIPRQ LPGSHSEAGV QGLSAGDDSE LGSHCVAQTG LELLASGDPL PSASQNAEMI ETGSDCVTQ AGLQLLASSD PPALASKNAE VTGTMSQDTE VDMKEVELNE LEPEKQPMNA ASGAAMSLAG AEKNGLVKIK V AEDEAEAA ...String:
HHHHHHHHHH SGRELQPPEA SIAVVSIPRQ LPGSHSEAGV QGLSAGDDSE LGSHCVAQTG LELLASGDPL PSASQNAEMI ETGSDCVTQ AGLQLLASSD PPALASKNAE VTGTMSQDTE VDMKEVELNE LEPEKQPMNA ASGAAMSLAG AEKNGLVKIK V AEDEAEAA AAAKFTGLSK EELLKVAGSP GWVRTRWALL LLFWLGWLGM LAGAVVIIVR APRCRELPAQ KWWHTGALYR IG DLQAFQG HGAGNLAGLK GRLDYLSSLK VKGLVLGPIH KNQKDDVAQT DLLQIDPNFG SKEDFDSLLQ SAKKKSIRVI LDL TPNYRG ENSWFSTQVD TVATKVKDAL EFWLQAGVDG FQVRDIENLK DASSFLAEWQ NITKGFSEDR LLIAGTNSSD LQQI LSLLE SNKDLLLTSS YLSDSGSTGE HTKSLVTQYL NATGNRWCSW SLSQARLLTS FLPAQLLRLY QLMLFTLPGT PVFSY GDEI GLDAAALPGQ PMEAPVMLWD ESSFPDIPGA VSANMTVKGQ SEDPGSLLSL FRRLSDQRSK ERSLLHGDFH AFSAGP GLF SYIRHWDQNE RFLVVLNFGD VGLSAGLQAS DLPASASLPA KADLLLSTQP GREEGSPLEL ERLKLEPHEG LLLRFPY AA TGA

UniProtKB: Amino acid transporter heavy chain SLC3A2

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Macromolecule #2: Y+L amino acid transporter 1

MacromoleculeName: Y+L amino acid transporter 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.963137 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKSG PDEVDASGRV DSTEYEVASQ PEVETSPLGD GASPGPEQVK LKKEISLLNG VCLIVGNMIG SGIFVSPKGV LIYSASFGL SLVIWAVGGL FSVFGALCYA ELGTTIKKSG ASYAYILEAF GGFLAFIRLW TSLLIIEPTS QAIIAITFAN Y MVQPLFPS ...String:
DYKDDDDKSG PDEVDASGRV DSTEYEVASQ PEVETSPLGD GASPGPEQVK LKKEISLLNG VCLIVGNMIG SGIFVSPKGV LIYSASFGL SLVIWAVGGL FSVFGALCYA ELGTTIKKSG ASYAYILEAF GGFLAFIRLW TSLLIIEPTS QAIIAITFAN Y MVQPLFPS CFAPYAASRL LAAACICLLT FINCAYVKWG TLVQDIFTYA KVLALIAVIV AGIVRLGQGA STHFENSFEG SS FAVGDIA LALYSALFSY SGWDTLNYVT EEIKNPERNL PLSIGISMPI VTIIYILTNV AYYTVLDMRD ILASDAVAVT FAD QIFGIF NWIIPLSVAL SCFGGLNASI VAASRLFFVG SREGHLPDAI CMIHVERFTP VPSLLFNGIM ALIYLCVEDI FQLI NYYSF SYWFFVGLSI VGQLYLRWKE PDRPRPLKLS VFFPIVFCLC TIFLVAVPLY SDTINSLIGI AIALSGLPFY FLIIR VPEH KRPLYLRRIV GSATRYLQVL CMSVAAEMDL EDGGEMPKQR DPKSN

UniProtKB: Y+L amino acid transporter 1

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Macromolecule #4: ARGININE

MacromoleculeName: ARGININE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ARG
Molecular weightTheoretical: 175.209 Da
Chemical component information

ChemComp-ARG:
ARGININE

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 343068
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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