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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: To Be Published
Title: Structural insights into the amino acid transport and pharmacological blockade of human LAT4
Authors: Yin YX / Ding D / Lu YS
History
DepositionDec 17, 2024-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 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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