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- PDB-9v3z: SLC36A1 bound to D-NPA -

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Basic information

Entry
Database: PDB / ID: 9v3z
TitleSLC36A1 bound to D-NPA
ComponentsProton-coupled amino acid transporter 1
KeywordsTRANSPORT PROTEIN / lysosomal membrane protein NPA
Function / homology
Function and homology information


amino acid:proton symporter activity / ABC-type taurine transporter transporter activity / Proton-coupled neutral amino acid transporters / proline:proton symporter activity / L-alanine transport / proline transmembrane transport / glycine transmembrane transporter activity / L-proline transmembrane transporter activity / glycine transport / L-alanine transmembrane transporter activity ...amino acid:proton symporter activity / ABC-type taurine transporter transporter activity / Proton-coupled neutral amino acid transporters / proline:proton symporter activity / L-alanine transport / proline transmembrane transport / glycine transmembrane transporter activity / L-proline transmembrane transporter activity / glycine transport / L-alanine transmembrane transporter activity / alanine transmembrane transporter activity / alanine transport / taurine transmembrane transport / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / vacuolar membrane / amino acid transport / amino acid import across plasma membrane / proton transmembrane transport / apical plasma membrane / lysosomal membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein
Similarity search - Domain/homology
: / Proton-coupled amino acid transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang, S.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21532004, 31570733 China
CitationJournal: Nat Commun / Year: 2026
Title: Substrate recognition and transport mechanism of the human proton-coupled amino-acid transporter 1 (SLC36A1).
Authors: Jian Yin / Sensen Zhang / Chang Liu / Min Xie / Yuanzhu Gao / Maofei Chen / Yixue Wang / Meiying Chen / Hongxuan Fan / Zi Yang / Huan Li / Li Liang / Boda Zhou / Xudong Chen / Maojun Yang /
Abstract: The proton-coupled amino-acid transporter SLC36A1 (hPAT1) is an atypical H⁺-driven carrier and mediates the intestinal absorption of a wide array of zwitterionic amino-acid analogs, including many ...The proton-coupled amino-acid transporter SLC36A1 (hPAT1) is an atypical H⁺-driven carrier and mediates the intestinal absorption of a wide array of zwitterionic amino-acid analogs, including many compounds with central nervous-system (CNS) activity, as well as the activation of the mTORC1 pathway and the export of amino acids from lysosomes, thereby maintaining cellular amino-acid homeostasis. Here, we present the cryo-EM structures of a member of the SLC36 family, hPAT1, in its apo state and in complex with three chemically distinct substrates, including the α-amino acid D-serine, the β-amino acid nipecotic acid, and the heterocyclic drug D-cycloserine, at resolutions of 3.4-3.5 Å. Despite their chemical diversity, all ligands adopt a spatially convergent binding mode, elucidating the structural basis for PAT1's broad substrate promiscuity. In addition, we identify E270 as a potential proton-binding site. Together, these findings provide structural insights into the molecular mechanism of proton-coupled amino acid transport. Notably, the cryo-EM structure of PAT1 bound to D-cycloserine illustrates a viable oral CNS drug delivery strategy: exploiting polar scaffolds to achieve transporter-mediated intestinal absorption and blood-brain barrier penetration without relying on high lipophilicity.
History
DepositionMay 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proton-coupled amino acid transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4633
Polymers53,1121
Non-polymers3502
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Proton-coupled amino acid transporter 1 / Proton/amino acid transporter 1 / hPAT1 / Solute carrier family 36 member 1


Mass: 53112.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC36A1, PAT1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q7Z2H8
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-A1BDB / (3S)-piperidine-3-carboxylic acid


Mass: 129.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO2
Has ligand of interestN
Has protein modificationY

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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: lysosomal membrane protein with NPA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 477000 / Symmetry type: POINT

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