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- EMDB-62783: Structure of ENBT1 in the apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-62783
TitleStructure of ENBT1 in the apo state
Map datasharpened map of ENBT1 in the apo state
Sample
  • Complex: Equilibrative nucleobase transporter 1
    • Protein or peptide: Equilibrative nucleobase transporter 1
  • Ligand: water
KeywordsENBT1 / SLC43A3 / amino acid transporter / MEMBRANE PROTEIN
Function / homologyEquilibrative nucleobase transporter 1 / adenine transmembrane transporter activity / guanine transmembrane transporter activity / hypoxanthine transport / fatty acid transmembrane transporter activity / xenobiotic transmembrane transporter activity / MFS transporter superfamily / basolateral plasma membrane / Equilibrative nucleobase transporter 1
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYin YX / Ding D / Lu YS
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030081 China
National Natural Science Foundation of China (NSFC)81874235 China
National Natural Science Foundation of China (NSFC)82173386 China
CitationJournal: EMBO J / Year: 2026
Title: Structures of the neutral amino acid transporter LAT4 provide insights into antitumor effects of its inhibitor tubeimoside-1.
Authors: Dian Ding / Yishuo Lu / Jingyi Yang / Hongyi Chen / Peijun Jiang / Yan Jin / Jianyuan Luo / Guangxi Wang / Yuxin Yin /
Abstract: Methionine restriction has emerged as a promising strategy for extending lifespan and enhancing cancer therapy. LAT4, an amino acid transporter encoded by SLC43A2, is frequently overexpressed in ...Methionine restriction has emerged as a promising strategy for extending lifespan and enhancing cancer therapy. LAT4, an amino acid transporter encoded by SLC43A2, is frequently overexpressed in multiple cancers and critically contributes to systemic methionine accumulation. However, the structural basis of LAT4 function remains poorly understood, and no effective inhibitors have been developed to date. In this study, we present high-resolution cryo-electron microscopy structures of LAT4 and the related SLC43A3-encoded purine transporter ENBT1. The phenylalanine-bound structure of LAT4 enables the characterization of the substrate binding pocket. Comparison of the outward-facing ENBT1 and inward-facing LAT4 structures identifies key residues involved in the methionine transport process. Structural analysis of digitonin binding to the central cavity of LAT4 enabled identification of tubeimoside-1 (TBM-1) as a potent inhibitor of LAT4-mediated methionine uptake. We demonstrate that tubeimoside-1 reduces methionine uptake in B16F10 cancer cells. Furthermore, TBM-1 suppresses tumor progression in the MMTV-PyVT mouse model of breast cancer through systemic methionine restriction. Our study provides insights into the LAT4 transport mechanism and identifies tubeimoside-1 as a potent inhibitor of methionine uptake and establishes a foundation for developing LAT4-targeting therapeutics to restrict methionine uptake.
History
DepositionDec 17, 2024-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62783.png

Downloads & links

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Map

FileDownload / File: emd_62783.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of ENBT1 in the apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 250.2 Å		0.83 Å/pix.
x 300 pix.
= 250.2 Å		0.83 Å/pix.
x 300 pix.
= 250.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.9995393 - 1.5602337
Average (Standard dev.)-0.0010003897 (±0.02442145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 250.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: map of ENBT1 in the apo state

Fileemd_62783_additional_1.map
Annotationmap of ENBT1 in the apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-a map of ENBT1 in the apo state

Fileemd_62783_half_map_1.map
Annotationhalf-a map of ENBT1 in the apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-b map of ENBT1 in the apo state

Fileemd_62783_half_map_2.map
Annotationhalf-b map of ENBT1 in the apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Equilibrative nucleobase transporter 1

EntireName: Equilibrative nucleobase transporter 1
Components
  • Complex: Equilibrative nucleobase transporter 1
    • Protein or peptide: Equilibrative nucleobase transporter 1
  • Ligand: water

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Supramolecule #1: Equilibrative nucleobase transporter 1

SupramoleculeName: Equilibrative nucleobase transporter 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Equilibrative nucleobase transporter 1

MacromoleculeName: Equilibrative nucleobase transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.572488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGQGLPLHV ATLLTGLLEC LGFAGVLFGW PSLVFVFKNE DYFKDLCGPD AGPIGNATGQ ADCKAQDERF SLIFTLGSFM NNFMTFPTG YIFDRFKTTV ARLIAIFFYT TATLIIAFTS AGSAVLLFLA MPMLTIGGIL FLITNLQIGN LFGQHRSTII T LYNGAFDS ...String:
MAGQGLPLHV ATLLTGLLEC LGFAGVLFGW PSLVFVFKNE DYFKDLCGPD AGPIGNATGQ ADCKAQDERF SLIFTLGSFM NNFMTFPTG YIFDRFKTTV ARLIAIFFYT TATLIIAFTS AGSAVLLFLA MPMLTIGGIL FLITNLQIGN LFGQHRSTII T LYNGAFDS SSAVFLIIKL LYEKGISLRA SFIFISVCST WHVARTFLLM PRGHIPYPLP PNYSYGLCPG NGTTKEEKET AE HENRELQ SKEFLSAKEE TPGAGQKQEL RSFWSYAFSR RFAWHLVWLS VIQLWHYLFI GTLNSLLTNM AGGDMARVST YTN AFAFTQ FGVLCAPWNG LLMDRLKQKY QKEARKTGSS TLAVALCSTV PSLALTSLLC LGFALCASVP ILPLQYLTFI LQVI SRSFL YGSNAAFLTL AFPSEHFGKL FGLVMALSAV VSLLQFPIFT LIKGSLQNDP FYVNVMFMLA ILLTFFHPFL VYREC RTWK ESPSAIA

UniProtKB: Equilibrative nucleobase transporter 1

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 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: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 266732
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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