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- EMDB-36254: Structure of the auxin exporter PIN1 in Arabidopsis thaliana in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-36254
TitleStructure of the auxin exporter PIN1 in Arabidopsis thaliana in the Naproxen-bound state
Map data
Sample
  • Complex: Binary complex of PIN1 with nanobody
    • Protein or peptide: Auxin efflux carrier component 1
    • Protein or peptide: nanobody
  • Ligand: (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid
Keywordsmembrane transporter / PLANT PROTEIN
Function / homology
Function and homology information


cotyledon morphogenesis / leaf formation / cotyledon development / leaf shaping / shoot system development / xylem and phloem pattern formation / inflorescence development / gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity ...cotyledon morphogenesis / leaf formation / cotyledon development / leaf shaping / shoot system development / xylem and phloem pattern formation / inflorescence development / gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / auxin polar transport / plant-type cell wall / flower development / root development / photomorphogenesis / embryo development ending in seed dormancy / auxin-activated signaling pathway / plasmodesma / basal plasma membrane / cell periphery / apical part of cell / apical plasma membrane / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Auxin efflux carrier, plant type / : / Membrane transport protein / Membrane transport protein
Similarity search - Domain/homology
Auxin efflux carrier component 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSun L / Liu X / Yang Z / Xia J
Funding support China, 3 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020103 China
National Natural Science Foundation of China (NSFC)31900885 China
National Natural Science Foundation of China (NSFC)31870732 China
CitationJournal: Plant Commun / Year: 2023
Title: Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen.
Authors: Jing Xia / Mengjuan Kong / Zhisen Yang / Lianghanxiao Sun / Yakun Peng / Yanbo Mao / Hong Wei / Wei Ying / Yongxiang Gao / Jiří Friml / Jianping Weng / Xin Liu / Linfeng Sun / Shutang Tan /
Abstract: The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and ...The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture.
History
DepositionMay 22, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36254.png

Downloads & links

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Map

FileDownload / File: emd_36254.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.47
Minimum - Maximum-2.089839 - 3.1177664
Average (Standard dev.)0.0026055318 (±0.07875225)
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_36254_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36254_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of PIN1 with nanobody

EntireName: Binary complex of PIN1 with nanobody
Components
  • Complex: Binary complex of PIN1 with nanobody
    • Protein or peptide: Auxin efflux carrier component 1
    • Protein or peptide: nanobody
  • Ligand: (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid

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Supramolecule #1: Binary complex of PIN1 with nanobody

SupramoleculeName: Binary complex of PIN1 with nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Auxin efflux carrier component 1

MacromoleculeName: Auxin efflux carrier component 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 67.080781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MITAADFYHV MTAMVPLYVA MILAYGSVKW WKIFTPDQCS GINRFVALFA VPLLSFHFIA ANNPYAMNLR FLAADSLQKV IVLSLLFLW CKLSRNGSLD WTITLFSLST LPNTLVMGIP LLKGMYGNFS GDLMVQIVVL QCIIWYTLML FLFEYRGAKL L ISEQFPDT ...String:
MITAADFYHV MTAMVPLYVA MILAYGSVKW WKIFTPDQCS GINRFVALFA VPLLSFHFIA ANNPYAMNLR FLAADSLQKV IVLSLLFLW CKLSRNGSLD WTITLFSLST LPNTLVMGIP LLKGMYGNFS GDLMVQIVVL QCIIWYTLML FLFEYRGAKL L ISEQFPDT AGSIVSIHVD SDIMSLDGRQ PLETEAEIKE DGKLHVTVRR SNASRSDIYS RRSQGLSATP RPSNLTNAEI YS LQSSRNP TPRGSSFNHT DFYSMMASGG GRNSNFGPGE AVFGSKGPTP RPSNYEEDGG PAKPTAAGTA AGAGRFHYQS GGS GGGGGA HYPAPNPGMF SPNTGGGGGT AAKGNAPVVG GKRQDGNGRD LHMFVWSSSA SPVSDVFGGG GGNHHADYST ATND HQKDV KISVPQGNSN DNQYVEREEF SFGNKDDDSK VLATDGGNNI SNKTTQAKVM PPTSVMTRLI LIMVWRKLIR NPNSY SSLF GITWSLISFK WNIEMPALIA KSISILSDAG LGMAMFSLGL FMALNPRIIA CGNRRAAFAA AMRFVVGPAV MLVASY AVG LRGVLLHVAI IQAALPQGIV PFVFAKEYNV HPDILSTAVI FGMLIALPIT LLYYILLGL

UniProtKB: Auxin efflux carrier component 1

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Macromolecule #2: nanobody

MacromoleculeName: nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.337863 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSSQVQLVE SGGGLVQAGG SLRLSCAASG FPVDITWMEW YRQAPGKERE WVAAIYSSGQ STWYADSVKG RFTISRDNAK NTVYLQMNS LKPEDTAVYY CRVKVGAWYK GQGTQVTVSA GRAG

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Macromolecule #3: (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid

MacromoleculeName: (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / type: ligand / ID: 3 / Number of copies: 2 / Formula: NPS
Molecular weightTheoretical: 230.259 Da
Chemical component information

ChemComp-NPS:
(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / antiinflammatory*YM

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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

MicroscopeFEI TITAN 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: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7y9t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48551
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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