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- PDB-8jh5: Structure of the auxin exporter PIN1 in Arabidopsis thaliana in t... -

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Basic information

Entry
Database: PDB / ID: 8jh5
TitleStructure of the auxin exporter PIN1 in Arabidopsis thaliana in the Naproxen-bound state
Components
  • Auxin efflux carrier component 1
  • nanobody
KeywordsPLANT PROTEIN / membrane transporter
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 / auxin-activated signaling pathway / embryo development ending in seed dormancy / 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
(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / Auxin efflux carrier component 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSun, L. / Liu, X. / Yang, Z. / Xia, J.
Funding support China, 3items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Auxin efflux carrier component 1
C: nanobody
D: nanobody
B: Auxin efflux carrier component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,2986
Polymers160,8374
Non-polymers4612
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 efflux carrier component 1 / Protein PIN-FORMED / AtPIN1


Mass: 67080.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PIN1, At1g73590, F6D5.2 / Plasmid: pCAG / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: Q9C6B8
#2: Antibody nanobody


Mass: 13337.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-NPS / (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / NAPROXEN


Mass: 230.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory*YM
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: Binary complex of PIN1 with nanobody / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48551 / Symmetry type: POINT

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