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- EMDB-61326: Structure of LAT4 in complex with digitonin -

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Basic information

Entry
Database: EMDB / ID: EMD-61326
TitleStructure of LAT4 in complex with digitonin
Map datasharpened map of LAT4 in complex with digitonin
Sample
  • Complex: Large neutral amino acids transporter small subunit 4
    • Protein or peptide: Large neutral amino acids transporter small subunit 4
  • Ligand: Digitonin
KeywordsLAT4 / SLC43A2 / amino acid transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of amino acid transport / negative regulation of L-leucine import across plasma membrane / L-phenylalanine transmembrane transporter activity / L-methionine transmembrane transporter activity / L-isoleucine transmembrane transporter activity / phenylalanine transport / methionine transport / L-leucine transmembrane transporter activity / isoleucine transport / L-amino acid transmembrane transporter activity ...negative regulation of amino acid transport / negative regulation of L-leucine import across plasma membrane / L-phenylalanine transmembrane transporter activity / L-methionine transmembrane transporter activity / L-isoleucine transmembrane transporter activity / phenylalanine transport / methionine transport / L-leucine transmembrane transporter activity / isoleucine transport / L-amino acid transmembrane transporter activity / L-leucine transport / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / amino acid transport / basolateral plasma membrane / plasma membrane
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / MFS transporter superfamily
Similarity search - Domain/homology
Large neutral amino acids transporter small subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYin YX / Ding D / Lu YS / Chen HY
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 / Chen HY
History
DepositionAug 27, 2024-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61326.png

Downloads & links

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Map

FileDownload / File: emd_61326.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of LAT4 in complex with digitonin
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: 0.155
Minimum - Maximum-0.6928811 - 1.0274794
Average (Standard dev.)-0.0005570327 (±0.01773567)
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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Half map: half-b map of LAT4 in complex with digitonin

Fileemd_61326_half_map_1.map
Annotationhalf-b map of LAT4 in complex with digitonin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-a map of LAT4 in complex with digitonin

Fileemd_61326_half_map_2.map
Annotationhalf-a map of LAT4 in complex with digitonin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Large neutral amino acids transporter small subunit 4

EntireName: Large neutral amino acids transporter small subunit 4
Components
  • Complex: Large neutral amino acids transporter small subunit 4
    • Protein or peptide: Large neutral amino acids transporter small subunit 4
  • Ligand: Digitonin

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Supramolecule #1: Large neutral amino acids transporter small subunit 4

SupramoleculeName: Large neutral amino acids transporter small subunit 4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Large neutral amino acids transporter small subunit 4

MacromoleculeName: Large neutral amino acids transporter small subunit 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.797562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPTLATAHR RRWWMACTAV LENLLFSAVL LGWGSLLIML KSEGFYSYLC TEPENVTNGT VGGTAEPGHE EVSWMNGWLS CQAQDEMLN LAFTVGSFLL SAITLPLGIV MDKYGPRKLR LLGSACFAVS CLLIAYGASK PNALSVLIFI ALALNGFGGM C MTFTSLTL ...String:
MAPTLATAHR RRWWMACTAV LENLLFSAVL LGWGSLLIML KSEGFYSYLC TEPENVTNGT VGGTAEPGHE EVSWMNGWLS CQAQDEMLN LAFTVGSFLL SAITLPLGIV MDKYGPRKLR LLGSACFAVS CLLIAYGASK PNALSVLIFI ALALNGFGGM C MTFTSLTL PNMFGDLRST FIALMIGSYA SSAVTFPGIK LIYDAGVSFI VVLVVWAGCS GLVFLNCFFN WPLEPFPGPE DM DYSVKIK FSWLGFDHKI TGKQFYKQVT TVGRRLSVGS SMRSAKEQVA LQEGHKLCLS TVDLEVKCQP DAAVAPSFMH SVF SPILLL SLVTMCVTQL RLIFYMGAMN NILKFLVSGD QKTVGLYTSI FGVLQLLCLL TAPVIGYIMD WRLKECEDAS EEPE EKDAN QGEKKKKKRD RQIQKITNAM RAFAFTNLLL VGFGVTCLIP NLPLQILSFI LHTIVRGFIH SAVGGLYAAV YPSTQ FGSL TGLQSLISAL FALLQQPLFL AMMGPLQGDP LWVNVGLLLL SLLGFCLPLY LICYRRQLER QLQQRQEDDK LFLKIN GSS NQEAFV

UniProtKB: Large neutral amino acids transporter small subunit 4

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Macromolecule #2: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 2 / Number of copies: 1 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

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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

MicroscopeFEI TITAN 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 177241
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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