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- EMDB-63417: IAA-bound AUX1 -

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Basic information

Entry
Database: EMDB / ID: EMD-63417
TitleIAA-bound AUX1
Map data
Sample
  • Complex: AUX1
    • Protein or peptide: Auxin transporter protein 1
  • Ligand: 1H-INDOL-3-YLACETIC ACID
Keywordstransport / LeuT-fold / PROTEIN TRANSPORT
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 / symporter activity ...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 / symporter activity / amino acid transmembrane transporter activity / response to nematode / 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: 3.52 Å
AuthorsWang CC / Jing D / Kong F / Huang GXY / Shi YG
Funding support1 items
OrganizationGrant numberCountry
Other government2020C04001
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis of auxin binding and transport by AUX1.
Authors: Dan Jing / Fang Kong / Xiaoli Lu / Gaoxingyu Huang / Jing Huang / Haolin Wang / Yigong Shi / Chengcheng Wang /
Abstract: Indole-3-acetic acid (IAA), the major form of auxin, is essential for plant growth. Auxin resistant 1 (AUX1), the first identified auxin importer, plays a crucial role in polar auxin transport (PAT). ...Indole-3-acetic acid (IAA), the major form of auxin, is essential for plant growth. Auxin resistant 1 (AUX1), the first identified auxin importer, plays a crucial role in polar auxin transport (PAT). Here, we present cryo-EM structures of AUX1 in the IAA-free and IAA-bound states. AUX1 exists as a monomer that contains 11 transmembrane helices (TMs). TMs 1 to 5 and 6 to 10 constitute the two halves of a classic LeuT-fold, and TM11 interacts with both halves at the interface. In the IAA-bound state, IAA is specifically recognized in a central pocket formed by TM1, TM3, TM6, and TM8. In the presence of IAA, TM1 and TM6 undergo marked conformational changes that are critical for IAA transport. His249 stands out to be a key residue for substrate uptake and release. Our structures reveal the molecular basis for AUX1-mediated IAA binding and transport.
History
DepositionFeb 12, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63417.png

Downloads & links

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Map

FileDownload / File: emd_63417.map.gz / Format: CCP4 / Size: 27 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.)
1.08 Å/pix.
x 192 pix.
= 206.842 Å		1.08 Å/pix.
x 192 pix.
= 206.842 Å		1.08 Å/pix.
x 192 pix.
= 206.842 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-9.684945000000001 - 16.859317999999998
Average (Standard dev.)0.0013421454 (±0.15661648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 206.84158 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63417_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_63417_half_map_1.map
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Half map: #2

Fileemd_63417_half_map_2.map
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Sample components

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Entire : AUX1

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

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Supramolecule #1: AUX1

SupramoleculeName: AUX1 / 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: 57.131629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHH HGSVEDYKDD DDKGSMSEGV EAIVANDNGT DQVNGNRTGK DNEEHDGSTG SNLSNFLWHG GSVWDAWFSC ASNQVAQVL LTLPYSFSQL GMLSGIVLQI FYGLLGSWTA YLISVLYVEY RARKEKEGKS FKNHVIQWFE VLDGLLGSYW K ALGLAFNC ...String:
MHHHHHHHHH HGSVEDYKDD DDKGSMSEGV EAIVANDNGT DQVNGNRTGK DNEEHDGSTG SNLSNFLWHG GSVWDAWFSC ASNQVAQVL LTLPYSFSQL GMLSGIVLQI FYGLLGSWTA YLISVLYVEY RARKEKEGKS FKNHVIQWFE VLDGLLGSYW K ALGLAFNC TFLLFGSVIQ LIACASNIYY INDHLDKRTW TYIFGACCAT TVFIPSFHNY RIWSFLGLGM TTYTAWYLAI AS IIHGQAE GVKHSGPTKL VLYFTGATNI LYTFGGHAVT VEIMHAMWKP QKFKYIYLMA TLYVFTLTIP SAAAVYWAFG DAL LDHSNA FSLMPKNAWR DAAVILMLIH QFITFGFACT PLYFVWEKVI GMHDTKSICL RALARLPVVI PIWFLAIIFP FFGP INSAV GALLVSFTVY IIPSLAHMLT YRSASARQNA AEKPPFFMPS WTAMYVLNAF VVVWVLIVGF GFGGWASVTN FVRQV DTFG LFAKCYQCKP AAAAAHAPVS ALHHRL

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

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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
Sugar embeddingMaterial: LMNG/CHS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131289
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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