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- EMDB-61398: Structure of the auxin importer AUX1 in Arabidopsis thaliana in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-61398
TitleStructure of the auxin importer AUX1 in Arabidopsis thaliana in the IAA-bound state
Map data
Sample
  • Complex: AUX1 protein in complex with IAA
    • Protein or peptide: Auxin transporter protein 1
  • Ligand: 1H-INDOL-3-YLACETIC ACID
  • Ligand: water
KeywordsAuxin / importer / AUX1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


root hair cell differentiation / auxin binding / root cap development / somatic embryogenesis / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / establishment of planar polarity / auxin polar transport / amino acid transmembrane transport ...root hair cell differentiation / auxin binding / root cap development / somatic embryogenesis / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / establishment of planar polarity / auxin polar transport / amino acid transmembrane transport / auxin-activated signaling pathway / response to nematode / symporter activity / amino acid transmembrane transporter activity / endosome / cell surface / Golgi apparatus / plasma membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein
Similarity search - Domain/homology
Auxin transporter protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSun L / Liu X / Wei H / Yang Z
Funding support China, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32322041 China
National Science Foundation (NSF, China)32321001 China
National Science Foundation (NSF, China)31900885 China
CitationJournal: Cell / Year: 2025
Title: Structural insights into auxin influx mediated by the Arabidopsis AUX1.
Authors: Zhisen Yang / Hong Wei / Yulin Gan / Huihui Liu / Yang Cao / Huihui An / Xiuzheng Que / Yongxiang Gao / Lizhe Zhu / Shutang Tan / Xin Liu / Linfeng Sun /
Abstract: Auxin is crucial in orchestrating diverse aspects of plant growth and development and modulating responses to environmental signals. The asymmetric spatiotemporal distribution of auxin generates ...Auxin is crucial in orchestrating diverse aspects of plant growth and development and modulating responses to environmental signals. The asymmetric spatiotemporal distribution of auxin generates local gradient patterns, which are regulated by both cellular auxin influx and efflux. The AUXIN1/LIKE-AUX1 (AUX1/LAX) family transporters have been identified as major auxin influx carriers. Here, we characterize the auxin uptake mediated by AUX1 from Arabidopsis thaliana. Using cryoelectron microscopy (cryo-EM), we determine its structure in three states: the auxin-unbound, the auxin-bound, and the competitive inhibitor, 3-chloro-4-hydroxyphenylacetic acid (CHPAA)-bound state. All structures adopt an inward-facing conformation. In the auxin-bound structure, indole-3-acetic acid (IAA) is coordinated to AUX1 primarily through hydrogen bonds with its carboxyl group. The functional roles of key residues in IAA binding are validated by in vitro and in planta analyses. CHPAA binds to the same site as IAA. These findings advance our understanding of auxin transport in plants.
History
DepositionSep 1, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61398.png

Downloads & links

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Map

FileDownload / File: emd_61398.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.090002 - 3.0514936
Average (Standard dev.)0.0005620837 (±0.056575257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61398_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61398_half_map_2.map
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Sample components

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Entire : AUX1 protein in complex with IAA

EntireName: AUX1 protein in complex with IAA
Components
  • Complex: AUX1 protein in complex with IAA
    • Protein or peptide: Auxin transporter protein 1
  • Ligand: 1H-INDOL-3-YLACETIC ACID
  • Ligand: water

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Supramolecule #1: AUX1 protein in complex with IAA

SupramoleculeName: AUX1 protein in complex with IAA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Auxin transporter protein 1

MacromoleculeName: Auxin transporter protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 54.10552 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEGVEAIVA NDNGTDQVNG NRTGKDNEEH DGSTGSNLSN FLWHGGSVWD AWFSCASNQV AQVLLTLPYS FSQLGMLSGI VLQIFYGLL GSWTAYLISV LYVEYRARKE KEGKSFKNHV IQWFEVLDGL LGSYWKALGL AFNCTFLLFG SVIQLIACAS N IYYINDHL ...String:
MSEGVEAIVA NDNGTDQVNG NRTGKDNEEH DGSTGSNLSN FLWHGGSVWD AWFSCASNQV AQVLLTLPYS FSQLGMLSGI VLQIFYGLL GSWTAYLISV LYVEYRARKE KEGKSFKNHV IQWFEVLDGL LGSYWKALGL AFNCTFLLFG SVIQLIACAS N IYYINDHL DKRTWTYIFG ACCATTVFIP SFHNYRIWSF LGLGMTTYTA WYLAIASIIH GQAEGVKHSG PTKLVLYFTG AT NILYTFG GHAVTVEIMH AMWKPQKFKY IYLMATLYVF TLTIPSAAAV YWAFGDALLD HSNAFSLMPK NAWRDAAVIL MLI HQFITF GFACTPLYFV WEKVIGMHDT KSICLRALAR LPVVIPIWFL AIIFPFFGPI NSAVGALLVS FTVYIIPSLA HMLT YRSAS ARQNAAEKPP FFMPSWTAMY VLNAFVVVWV LIVGFGFGGW ASVTNFVRQV DTFGLFAKCY QCKPAAAAAH APVSA LHHR L

UniProtKB: Auxin transporter protein 1

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Macromolecule #2: 1H-INDOL-3-YLACETIC ACID

MacromoleculeName: 1H-INDOL-3-YLACETIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: IAC
Molecular weightTheoretical: 175.184 Da
Chemical component information

ChemComp-IAC:
1H-INDOL-3-YLACETIC ACID / hormone*YM

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66531
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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