[English] 日本語
Yorodumi
- PDB-9h61: Auxin transporter-like protein 3 (LAX3) in the inward occluded st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h61
TitleAuxin transporter-like protein 3 (LAX3) in the inward occluded state in complex with auxin (Indole-3-acetic acid, IAA)
ComponentsAuxin transporter-like protein 3
KeywordsMEMBRANE PROTEIN / Auxin transmembrane transport / AAAP family / APC superfamily
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
1H-INDOL-3-YLACETIC ACID / Auxin transporter-like protein 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsUng, K.L. / Andersen, C.G. / Stokes, D.L. / Pedersen, B.P.
Funding supportEuropean Union, Denmark, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Auxin transporter-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6182
Polymers49,4431
Non-polymers1751
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Auxin transporter-like protein 3 / AUX1-like protein 3


Mass: 49442.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LAX3, At1g77690, T32E8.2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9CA25
#2: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: LAX3 with IAA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.049 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2150 mMSodium chlorideNaCl1
30.001 %LMNGC47H88O221
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Wait 4 seconds after sample loading, Blotting time 4 seconds with blotting force of -1 before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector modelNum. of grids imagedNum. of real imagesDetails
1159.3GATAN K3 BIOQUANTUM (6k x 4k)113772Dataset 1
2160GATAN K3 BIOQUANTUM (6k x 4k)114171Dataset 2
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scans
Sampling size (µm)WidthHeightIDImage recording-IDEntry-ID
557604092119H61
557604092229H61

-
Processing

EM software
IDNameVersionCategory
1EPUimage acquisition
12Cootmodel fitting
19PHENIX1.19.2_4158:model refinement
CTF correctionDetails: CTF amplitude correction was performed following motion correction using cryosparc-live
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4432384
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74645 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 111.9 / Space: REAL
Atomic model buildingAccession code: Q9CA25 / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023418
ELECTRON MICROSCOPYf_angle_d0.4274663
ELECTRON MICROSCOPYf_dihedral_angle_d3.686455
ELECTRON MICROSCOPYf_chiral_restr0.033523
ELECTRON MICROSCOPYf_plane_restr0.005566

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more