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- EMDB-51896: Auxin transporter-like protein 3 (LAX3) in the fully occluded sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-51896
TitleAuxin transporter-like protein 3 (LAX3) in the fully occluded state in complex with 2-naphthoxyacetic acid (2-NOA)
Map data
Sample
  • Complex: LAX3 with 2-NOA
    • Protein or peptide: Auxin transporter-like protein 3
  • Ligand: 2-naphthalen-2-yloxyethanoic acid
  • Ligand: water
KeywordsAuxin transmembrane transport / AAAP family / APC superfamily / MEMBRANE PROTEIN
Function / homology
Function and homology information


root cap development / lateral root formation / auxin influx transmembrane transporter activity / auxin polar transport / response to auxin / auxin-activated signaling pathway / symporter activity / amino acid transport / plasma membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein
Similarity search - Domain/homology
Auxin transporter-like protein 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsUng KL / Andersen CG / Stokes DL / Pedersen BP
Funding supportEuropean Union, Denmark, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101000936European Union
Novo Nordisk FoundationNNF23OC0086406 Denmark
CitationJournal: Nat Plants / Year: 2025
Title: Structures and mechanism of the AUX/LAX transporters involved in auxin import.
Authors: Kien Lam Ung / Lukas Schulz / Lorena Zuzic / Bjørn Lildal Amsinck / Sarah Koutnik-Abele / Ines Benhammouche / Camilla Gottlieb Andersen / Lynette Nel / Birgit Schiøtt / David L Stokes / ...Authors: Kien Lam Ung / Lukas Schulz / Lorena Zuzic / Bjørn Lildal Amsinck / Sarah Koutnik-Abele / Ines Benhammouche / Camilla Gottlieb Andersen / Lynette Nel / Birgit Schiøtt / David L Stokes / Ulrich Zeno Hammes / Bjørn Panyella Pedersen /
Abstract: Auxins are plant hormones that direct the growth and development of organisms on the basis of environmental cues. Indole-3-acetic acid (IAA) is the most abundant auxin in most plants. A variety of ...Auxins are plant hormones that direct the growth and development of organisms on the basis of environmental cues. Indole-3-acetic acid (IAA) is the most abundant auxin in most plants. A variety of membrane transport proteins work together to distribute auxins. These include the AUX/LAX protein family that mediate auxin import from the apoplast to the cytosol. Here we use structural and biophysical approaches combined with molecular dynamics to study transport by Arabidopsis thaliana LAX3, which is essential for plant root formation. Transport assays document high-affinity transport of IAA, as well as competitive behaviour of the synthetic phenoxyacetic acid auxin herbicide 2,4-dichlorophenoxyacetic acid and the auxin transport inhibitors 1-naphthoxyacetic acid and 2-naphthoxyacetic acid. Four cryo-EM structures were solved with resolutions of 2.9-3.4 Å: an inward open apo structure, two inward semi-occluded structures in complex with IAA and 2,4-dichlorophenoxyacetic acid, and a fully occluded structure in complex with 2-naphthoxyacetic acid. Structurally, LAX3 consists of a bundle and a scaffold domain. The ligand-binding site is sandwiched between these domains with two histidines occupying positions analogous to the sodium-binding sites in distantly related sodium:neurotransmitter transporters. This architecture suggests that these histidines couple transport to the proton motive force. Molecular dynamics simulations are used to explore substrate binding and release, including their dependence on specific protonation states. This study advances our understanding of auxin recognition and transport by AUX/LAX, providing insights into a fundamental aspect of plant physiology and development.
History
DepositionOct 23, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51896.png

Downloads & links

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Map

FileDownload / File: emd_51896.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 248.448 Å		0.65 Å/pix.
x 384 pix.
= 248.448 Å		0.65 Å/pix.
x 384 pix.
= 248.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.3013993 - 0.39652202
Average (Standard dev.)0.00003118907 (±0.007406394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 248.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51896_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51896_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51896_half_map_2.map
Projections & Slices
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Sample components

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Entire : LAX3 with 2-NOA

EntireName: LAX3 with 2-NOA
Components
  • Complex: LAX3 with 2-NOA
    • Protein or peptide: Auxin transporter-like protein 3
  • Ligand: 2-naphthalen-2-yloxyethanoic acid
  • Ligand: water

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Supramolecule #1: LAX3 with 2-NOA

SupramoleculeName: LAX3 with 2-NOA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 49 KDa

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Macromolecule #1: Auxin transporter-like protein 3

MacromoleculeName: Auxin transporter-like protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 49.44275 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGSVYDAWFS CASNQVAQVL LTLPYSFSQL GMMSGILFQL FYGLMGSWTA YLISVLYVEY RTRKEREKFD FRNHVIQWFE VLDGLLGKH WRNLGLIFNC TFLLFGSVIQ LIACASNIYY INDKLDKRTW TYIFGACCAT TVFIPSFHNY RIWSFLGLAM T TYTSWYLT ...String:
MGSVYDAWFS CASNQVAQVL LTLPYSFSQL GMMSGILFQL FYGLMGSWTA YLISVLYVEY RTRKEREKFD FRNHVIQWFE VLDGLLGKH WRNLGLIFNC TFLLFGSVIQ LIACASNIYY INDKLDKRTW TYIFGACCAT TVFIPSFHNY RIWSFLGLAM T TYTSWYLT IASLLHGQAE DVKHSGPTTM VLYFTGATNI LYTFGGHAVT VEIMHAMWKP QKFKAIYLLA TIYVLTLTLP SA SAVYWAF GDKLLTHSNA LSLLPKTGFR DTAVILMLIH QFITFGFAST PLYFVWEKLI GVHETKSMFK RAMARLPVVV PIW FLAIIF PFFGPINSAV GSLLVSFTVY IIPALAHMLT FAPAPSRENA VERPPRVVGG WMGTYCINIF VVVWVFVVGF GFGG WASMV NFVRQIDTFG LFTKCYQCPP HKPGENLYFQ

UniProtKB: Auxin transporter-like protein 3

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Macromolecule #2: 2-naphthalen-2-yloxyethanoic acid

MacromoleculeName: 2-naphthalen-2-yloxyethanoic acid / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1ISN
Molecular weightTheoretical: 202.206 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 8 / 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

Concentration8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloride
0.001 %C47H88O22LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Wait 4 seconds after sample loading, Blotting time 4 seconds with blotting force of -1 before plunging.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12748 / Average electron dose: 59.7 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: 0.6 µm / Nominal magnification: 130000
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: 3465533
CTF correctionSoftware - Name: cryoSPARC
Details: CTF amplitude correction was performed following motion correction using cryosparc-live
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49481
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC / Details: Cryosparc ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Cryosparc NU refinement
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

ca25


Chain - Chain ID: A / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot
RefinementSpace: REAL / Overall B value: 90
Output model

PDB-9h63:
Auxin transporter-like protein 3 (LAX3) in the fully occluded state in complex with 2-naphthoxyacetic acid (2-NOA)

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