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- EMDB-63360: Inward-open Structure of human B0AT1 -

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Basic information

Entry
Database: EMDB / ID: EMD-63360
TitleInward-open Structure of human B0AT1
Map data
Sample
  • Complex: Binary complex of B0AT1 and antibody
    • Protein or peptide: Sodium-dependent neutral amino acid transporter B(0)AT1
    • Protein or peptide: Antibody Fab Light chain
    • Protein or peptide: Antibody Fab Heavy chain
Keywordsamino acid transporter / SLC6 / TRANSPORT PROTEIN
Function / homology
Function and homology information


alanine:sodium symporter activity / Defective transport of neurotransmitters by SLC6A19 causes Hartnup disorder (HND) / Defective transport of amino acids by SLC6A19 causes Hartnup disorder (HND) / glycine:sodium symporter activity / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / SLC-mediated transport of neurotransmitters / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / neurotransmitter transport ...alanine:sodium symporter activity / Defective transport of neurotransmitters by SLC6A19 causes Hartnup disorder (HND) / Defective transport of amino acids by SLC6A19 causes Hartnup disorder (HND) / glycine:sodium symporter activity / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / SLC-mediated transport of neurotransmitters / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / neurotransmitter transport / amino acid transport / amino acid import across plasma membrane / viral life cycle / transmembrane transporter complex / response to nutrient / brush border membrane / sodium ion transmembrane transport / apical plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
Neutral amino acid SLC6 transporter / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Sodium-dependent neutral amino acid transporter B(0)AT1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsImazu T / Miyaguchi I / Hiraizumi M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2026
Title: Structure-guided development of a potent human BAT1 inhibitor effective in a mouse model of phenylketonuria.
Authors: Takuya Imazu / Tomoya Akashi / Masahiro Hiraizumi / Yosuke Inui / Wataru Sasaki / Tsuyoshi Takahashi / Hidenori Todoroki / Taichi Kumanomidou / Kazunori Yamada / Norie Fujikawa / Hiromi ...Authors: Takuya Imazu / Tomoya Akashi / Masahiro Hiraizumi / Yosuke Inui / Wataru Sasaki / Tsuyoshi Takahashi / Hidenori Todoroki / Taichi Kumanomidou / Kazunori Yamada / Norie Fujikawa / Hiromi Hisano / Hidetsugu Asada / Tsukasa Kusakizako / Tomohiro Nishizawa / So Iwata / Osamu Nureki / Ikuko Miyaguchi /
Abstract: BAT1 (SLC6A19) is a neutral amino acid transporter mediating intestinal absorption and renal reuptake of amino acids, including phenylalanine (Phe). Inhibiting BAT1 enhances Phe excretion, offering a ...BAT1 (SLC6A19) is a neutral amino acid transporter mediating intestinal absorption and renal reuptake of amino acids, including phenylalanine (Phe). Inhibiting BAT1 enhances Phe excretion, offering a therapeutic strategy for phenylketonuria (PKU). Using cryo-EM, we determined human BAT1 structures in outward- and inward-open states, revealing an allosteric pocket ~17 Å from the substrate site that is present in the outward-open conformation and has been previously reported. Structure-guided inhibitor design targeting this pocket produced a potent BAT1 inhibitor that locks the transporter in an outward-occluded state and blocks transport. The higher-resolution structures reveal detailed interactions at the binding site, including water-mediated coordination and conformational changes around Leu52. This inhibitor exhibited submicromolar IC against both human and mouse BAT1, and oral administration in PKU model mice increased urinary Phe and reduced plasma Phe levels. These findings provide structural insight into allosteric inhibition of BAT1 and establish a framework for the rational optimization of inhibitors targeting conformationally dynamic allosteric sites in SLC6-family transporters.
History
DepositionFeb 5, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63360.png

Downloads & links

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Map

FileDownload / File: emd_63360.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.0668356 - 0.11342894
Average (Standard dev.)-0.0000006823196 (±0.0024263333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63360_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63360_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of B0AT1 and antibody

EntireName: Binary complex of B0AT1 and antibody
Components
  • Complex: Binary complex of B0AT1 and antibody
    • Protein or peptide: Sodium-dependent neutral amino acid transporter B(0)AT1
    • Protein or peptide: Antibody Fab Light chain
    • Protein or peptide: Antibody Fab Heavy chain

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Supramolecule #1: Binary complex of B0AT1 and antibody

SupramoleculeName: Binary complex of B0AT1 and antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Sodium-dependent neutral amino acid transporter B(0)AT1

MacromoleculeName: Sodium-dependent neutral amino acid transporter B(0)AT1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.874625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNPGLDARIP SLAELETIEQ EEASSRPKWD NKAQYMLTCL GFCVGLGNVW RFPYLCQSHG GGAFMIPFLI LLVLLGIPLL YLEFAIGQR LRRGSLGVWS SIHPALKGIG LASMLTSFMV GLYYNTIISW IMWYLFNSFQ EPLPWSDCPL NENQTGYVDE C ARSSPVDY ...String:
MNPGLDARIP SLAELETIEQ EEASSRPKWD NKAQYMLTCL GFCVGLGNVW RFPYLCQSHG GGAFMIPFLI LLVLLGIPLL YLEFAIGQR LRRGSLGVWS SIHPALKGIG LASMLTSFMV GLYYNTIISW IMWYLFNSFQ EPLPWSDCPL NENQTGYVDE C ARSSPVDY FWYRETLNIS TSISDSGSIQ WWMLLCLACA WSVLYMCTIR GIETTGKAVY ITSTLPYVVL TIFLIRGLTL KG ATNGIVF LFTPNVTELA QPDTWLDAGA QVFFSFSLAF GGLISFASYN SVHNNCEKDS VIVSIINGFT SVYVAIVVYS VIG FRATQR YDDCFSTNIL TLINGFDLPE GNVTQENFVD MQQRCNASDP AAYAQLVFQT CDINAFLSEA VEGTGLAFIV FTEA ITKMP LSPLWSVLFF IMLFCLGLSS MFGNMEGVVV PLQDLRVIPP KWPKEVLTGL ICLGTFLIGL IFTLNSGQYW LSLLD SYAG SIPLLIIAFA EMFSVVWVYG VDRFNKDIEF MIGHKPNIFW QVTWRVVSPL LLLIIFLFFF VVEVSQELTY SIWDPG YEE FPKSQKISYP NWVYVVVVIV AGVPSLTIPG YAIYKLIRNH AQKPGDHQGL V

UniProtKB: Sodium-dependent neutral amino acid transporter B(0)AT1

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Macromolecule #2: Antibody Fab Light chain

MacromoleculeName: Antibody Fab Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.845598 KDa
SequenceString: AQAAELDIVM TQSPSSLVVS AGEKVTMTCK SSQSLFNSRT RKNYLAWYQQ KPGQSPKLLI YWASTRESGV PDRFTGSGSG TDFTLTISS VQAEDLAVYY CKQSSYLLTF GAGTKLELKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW K IDGSERQN ...String:
AQAAELDIVM TQSPSSLVVS AGEKVTMTCK SSQSLFNSRT RKNYLAWYQQ KPGQSPKLLI YWASTRESGV PDRFTGSGSG TDFTLTISS VQAEDLAVYY CKQSSYLLTF GAGTKLELKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW K IDGSERQN GVLNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNEC

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Macromolecule #3: Antibody Fab Heavy chain

MacromoleculeName: Antibody Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 36.524039 KDa
SequenceString: GGSSRSSLEV QLQQSGPELV KPGASVKISC KASGYTFTDY YINWVKQRPG QGLEWIGWIY PRSGGTKYIE KFKGKATLTV DTSSSTAYM QLNSLTSEDS AVYFCARFYY SYNEDYYALD YWSQGTSVTV SSAKTTAPSV YPLAPVCGDT SGSSVTLGCL V KGYFPEPV ...String:
GGSSRSSLEV QLQQSGPELV KPGASVKISC KASGYTFTDY YINWVKQRPG QGLEWIGWIY PRSGGTKYIE KFKGKATLTV DTSSSTAYM QLNSLTSEDS AVYFCARFYY SYNEDYYALD YWSQGTSVTV SSAKTTAPSV YPLAPVCGDT SGSSVTLGCL V KGYFPEPV TLTWNSGSLS SGVHTFPAVL QSDLYTLSSS VTVTSSTWPS QSITCNVAHP ASSTKVDKKI EPRGPTIKPC PP CKCPAPN LLGGPSVFIF PPKIKDVLMI SLSPIVTCVV VDVSEDDPDV QISWFVNNVE VHTAQTQTHR EDYNSTLRVV SAL PIQHQD WMSGKEFKC

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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: 7.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: PDB ENTRY
PDB model - PDB ID:

6m18

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 407749
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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