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- EMDB-64759: SLC36A1 bound to D-serine -

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Basic information

Entry
Database: EMDB / ID: EMD-64759
TitleSLC36A1 bound to D-serine
Map data
Sample
  • Complex: lysosomal membrane protein with ser
    • Protein or peptide: Proton-coupled amino acid transporter 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: D-SERINE
Keywordslysosomal membrane protein ser / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang SS
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64759.png

Downloads & links

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Map

FileDownload / File: emd_64759.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.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-1.5817621 - 2.6454976
Average (Standard dev.)-0.0027825534 (±0.049497414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64759_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_64759_half_map_2.map
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Sample components

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Entire : lysosomal membrane protein with ser

EntireName: lysosomal membrane protein with ser
Components
  • Complex: lysosomal membrane protein with ser
    • Protein or peptide: Proton-coupled amino acid transporter 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: D-SERINE

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Supramolecule #1: lysosomal membrane protein with ser

SupramoleculeName: lysosomal membrane protein with ser / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Proton-coupled amino acid transporter 1

MacromoleculeName: Proton-coupled amino acid transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.11223 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTQRLRNED YHDYSSTDVS PEESPSEGLN NLSSPGSYQR FGQSNSTTWF QTLIHLLKGN IGTGLLGLPL AVKNAGIVMG PISLLIIGI VAVHCMGILV KCAHHFCRRL NKSFVDYGDT VMYGLESSPC SWLRNHAHWG RRVVDFFLIV TQLGFCCVYF V FLADNFKQ ...String:
MSTQRLRNED YHDYSSTDVS PEESPSEGLN NLSSPGSYQR FGQSNSTTWF QTLIHLLKGN IGTGLLGLPL AVKNAGIVMG PISLLIIGI VAVHCMGILV KCAHHFCRRL NKSFVDYGDT VMYGLESSPC SWLRNHAHWG RRVVDFFLIV TQLGFCCVYF V FLADNFKQ VIEAANGTTN NCHNNETVIL TPTMDSRLYM LSFLPFLVLL VFIRNLRALS IFSLLANITM LVSLVMIYQF IV QRIPDPS HLPLVAPWKT YPLFFGTAIF SFEGIGMVLP LENKMKDPRK FPLILYLGMV IVTILYISLG CLGYLQFGAN IQG SITLNL PNCWLYQSVK LLYSIGIFFT YALQFYVPAE IIIPFFVSRA PEHCELVVDL FVRTVLVCLT CILAILIPRL DLVI SLVGS VSSSALALII PPLLEVTTFY SEGMSPLTIF KDALISILGF VGFVVGTYEA LYELIQPSNA PIFINSTCAF I

UniProtKB: Proton-coupled amino acid transporter 1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: D-SERINE

MacromoleculeName: D-SERINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: DSN
Molecular weightTheoretical: 105.093 Da
Chemical component information

ChemComp-DSN:
D-SERINE

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 345000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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