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- EMDB-55110: Cryo-EM structure of the Arabidopsis thaliana CAT4 transporter in... -

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Basic information

Entry
Database: EMDB / ID: EMD-55110
TitleCryo-EM structure of the Arabidopsis thaliana CAT4 transporter in the outward-open apo state (without synthetic nanobody)
Map dataSharpened map
Sample
  • Organelle or cellular component: Arabidopsis thaliana cationic amino acid transporter 4 solubilised in LMNG
    • Protein or peptide: Cationic amino acid transporter 4, vacuolar
Keywordscationic amino acid transporter / APC fold / LeuT fold / cholesterol / outward-open state / cationic amino acids / SLC7 / MEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homologyCationic amino acid transporter, C-terminal / C-terminus of AA_permease / plant-type vacuole membrane / Amino acid/polyamine transporter I / Amino acid permease / plant-type vacuole / amino acid transmembrane transporter activity / amino acid transport / Cationic amino acid transporter 4, vacuolar
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsKolokouris D / Zeng YC / Newstead S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011224/1 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for pH-responsive amino acid transport via SLC7A4.
Authors: Dimitrios Kolokouris / Anuja Bothra / Takafumi Kato / Yi C Zeng / Simon Lichtinger / Joanne L Parker / Philip C Biggin / Simon Newstead /
Abstract: The transport of amino acids across cell membranes is essential for metabolism, neuronal signalling, and immune system function. The amino acid polyamine organocation (APC) superfamily controls amino ...The transport of amino acids across cell membranes is essential for metabolism, neuronal signalling, and immune system function. The amino acid polyamine organocation (APC) superfamily controls amino acid transport via mechanisms including amino acid exchange, facilitative diffusion, and sodium- or proton-coupled transport. Although many mammalian APC members functioning as exchangers and sodium-coupled systems have been identified, the mechanisms underlying pH-regulated amino acid transport in mammalian cells remain unclear. Here, we show that the plasma membrane amino acid transporter SLC7A4 is regulated by low extracellular pH and functions as a leucine transporter in human cells. Using Cryo-EM structures of the plant homologue, CAT4, from Arabidopsis thaliana in outward-open apo and L-ornithine-bound states, as well as transport assays and molecular dynamics simulations based on homology models of the human transporter, we identify residues responsible for amino acid selectivity that supports an allosteric mechanism linking ligand recognition to pH regulation. This mechanism is consistent with an evolutionary link to proton-coupled prokaryotic homologues. Overall, our findings provide a structural and functional basis for pH-gated leucine transport by the human SLC7A4 transporter and provides a framework for understanding amino acid selectivity within the wider SLC7 family.
History
DepositionSep 22, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55110.png

Downloads & links

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Map

FileDownload / File: emd_55110.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.7098247 - 1.1885445
Average (Standard dev.)-0.00029730686 (±0.01983128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_55110_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_55110_half_map_2.map
AnnotationHalf Map B
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana cationic amino acid transporter 4 solubilise...

EntireName: Arabidopsis thaliana cationic amino acid transporter 4 solubilised in LMNG
Components
  • Organelle or cellular component: Arabidopsis thaliana cationic amino acid transporter 4 solubilised in LMNG
    • Protein or peptide: Cationic amino acid transporter 4, vacuolar

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Supramolecule #1: Arabidopsis thaliana cationic amino acid transporter 4 solubilise...

SupramoleculeName: Arabidopsis thaliana cationic amino acid transporter 4 solubilised in LMNG
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Cationic amino acid transporter 4, vacuolar

MacromoleculeName: Cationic amino acid transporter 4, vacuolar / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 63.680152 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNSLVRRKQV DSVHLIKNDG PHQLAKKLSA VDLVAIGVGT TIGAGVYILV GTVAREHTGP ALAVSFFIAG VAAALSACCY AELASRCPS AGSAYHYAYI CLGEGIAWLV GWALVLDYTI GGSAIARGIT PNLASFFGGL DNLPVFLARQ TIPGVGIVVD P CAALLIMI ...String:
MNSLVRRKQV DSVHLIKNDG PHQLAKKLSA VDLVAIGVGT TIGAGVYILV GTVAREHTGP ALAVSFFIAG VAAALSACCY AELASRCPS AGSAYHYAYI CLGEGIAWLV GWALVLDYTI GGSAIARGIT PNLASFFGGL DNLPVFLARQ TIPGVGIVVD P CAALLIMI VTILLCFGIK ESSTVQAIVT SVNVCTLVFI IVVGGYLACK TGWVGYDLPS GYFPFGLNGI LAGSAVVFFS YI GFDTVTS TAEEVKNPQR DLPLGIGIAL LICCILYMLL SVVIVGLVPY YSLNPDTPIS SAFGDSGMQW AAYILTTGAI TAL CASLLG SLLAQPRIFM AMARDGLLPA FFSEISPRTQ VPVKSTIAIG VLAAALAFFM DVAQLSEMVS VGTLMAFTAV AVCV LVLRY VPPDGVPLSS SSQTLSDTDE SRAETENFLV DAIESSDSPL LGNETARDEK YFGKRRKIAA WSIALVCIGV LGLAS AASA ERLPSFPRFT ICGVSAVILL GSLITLGYID EDEERHNFGH KGGFLCPFVP YLPVLCILIN TYLIINIGAG TWIRVL IWL LIGSMIYIFY GRSHSLLNNA VYVPTMTCTR KTTDHLA

UniProtKB: Cationic amino acid transporter 4, vacuolar

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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

Concentration4.7 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl, 150 mM NaCl, 0.003% w/v LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 30514 / Average exposure time: 2.6 sec. / Average electron dose: 39.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8226459
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 120868
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9hjk


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Chain A of 9HJK used for initial fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9sqh:
Cryo-EM structure of the Arabidopsis thaliana CAT4 transporter in the outward-open apo state (without synthetic nanobody)

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