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- PDB-9utd: influx carrier substrate bound form -

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Basic information

Entry
Database: PDB / ID: 9utd
Titleinflux carrier substrate bound form
ComponentsAuxin transporter protein 1
KeywordsHORMONE / hormone transporter
Function / homology
Function and homology information


root hair cell differentiation / auxin binding / root cap development / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / establishment of planar polarity / auxin polar transport / auxin-activated signaling pathway / response to nematode ...root hair cell differentiation / auxin binding / root cap development / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / establishment of planar polarity / auxin polar transport / auxin-activated signaling pathway / response to nematode / amino acid transmembrane transporter activity / symporter 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
(2,4-DICHLOROPHENOXY)ACETIC ACID / Auxin transporter protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsChen, H. / Jiang, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Plant / Year: 2025
Title: Structural basis of auxin recognition and transport by the plant influx carrier AUX1.
Authors: Huiwen Chen / Junping Fan / Cheng Chi / Jun Zhao / Di Wu / Xiaoguang Lei / Xing Wang Deng / Daohua Jiang /
Abstract: Auxin regulates numerous aspects of plant growth and development, featuring polar auxin transport mediated by auxin efflux and influx carriers. AUX1 is the major auxin importer that actively takes up ...Auxin regulates numerous aspects of plant growth and development, featuring polar auxin transport mediated by auxin efflux and influx carriers. AUX1 is the major auxin importer that actively takes up natural and synthetic auxins. However, the precise mechanisms underlying AUX1-mediated auxin recognition and transport remain elusive. Here, we present cryoelectron microscopy structures of Arabidopsis thaliana AUX1 in both apo and auxin-bound states, revealing the structural basis for auxin recognition. Structural analyses show that AUX1 assumes the LeuT-like fold in an inward-facing conformation and the auxin analog 2,4-D is recognized by polar residues located in the central cavity of AUX1. Furthermore, we identify a putative cation-binding site that contributes to stabilizing the inward-facing conformation. Interestingly, we reveal that His249 undergoes a substantial conformational shift, and its mutation completely abolishes transport activity, suggesting a crucial role for His249 in AUX1 gating. Collectively, this study provides a structural foundation for a deeper understanding of auxin influx by AUX1-like carriers.
History
DepositionMay 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Auxin transporter protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3503
Polymers54,1061
Non-polymers2442
Water00
1


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

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Components

#1: Protein Auxin transporter protein 1 / Auxin influx carrier protein 1 / Polar auxin transport inhibitor-resistant protein 1


Mass: 54105.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AUX1, AUX, PIR1, WAV5, At2g38120, F16M14.5 / Production host: Homo sapiens (human) / References: UniProt: Q96247
#2: Chemical ChemComp-CFA / (2,4-DICHLOROPHENOXY)ACETIC ACID / 2,4-DICHLOROPHENOXYACETIC ACID


Mass: 221.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Cl2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: plant influx carrier hormone bound form / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TITAN THEMIS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.17.1_3660 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129741 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063487
ELECTRON MICROSCOPYf_angle_d0.5994767
ELECTRON MICROSCOPYf_dihedral_angle_d15.386461
ELECTRON MICROSCOPYf_chiral_restr0.041531
ELECTRON MICROSCOPYf_plane_restr0.006579

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