9H63 | pdb_00009h63

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures and mechanism of the AUX/LAX transporters involved in auxin import.

Ung, K.L.Schulz, L.Zuzic, L.Amsinck, B.L.Koutnik-Abele, S.Benhammouche, I.Andersen, C.G.Nel, L.Schiott, B.Stokes, D.L.Hammes, U.Z.Pedersen, B.P.

(2025) Nat Plants 11: 1670-1680

  • DOI: https://doi.org/10.1038/s41477-025-02056-z
  • Primary Citation of Related Structures:  
    9H61, 9H62, 9H63, 9QQM

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Auxin transporter-like protein 3435Arabidopsis thalianaMutation(s): 0 
Gene Names: LAX3At1g77690T32E8.2
UniProt
Find proteins for Q9CA25 (Arabidopsis thaliana)
Explore Q9CA25 
Go to UniProtKB:  Q9CA25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CA25
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ISN (Subject of Investigation/LOI)
Query on A1ISN

Download Ideal Coordinates CCD File 
B [auth A]2-naphthalen-2-yloxyethanoic acid
C12 H10 O3
RZCJYMOBWVJQGV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101000936
Novo Nordisk FoundationDenmarkNNF23OC0086406

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references