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- PDB-7wkw: NPA bound state of AtPIN3 -

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Basic information

Entry
Database: PDB / ID: 7wkw
TitleNPA bound state of AtPIN3
ComponentsAuxin efflux carrier component 3
KeywordsTRANSPORT PROTEIN / PIN-FORMED (PIN) protein / NPA
Function / homology
Function and homology information


tropism / root hair initiation / auxin export across the plasma membrane / positive gravitropism / root hair elongation / auxin polar transport / gravitropism / root development / auxin-activated signaling pathway / vesicle membrane ...tropism / root hair initiation / auxin export across the plasma membrane / positive gravitropism / root hair elongation / auxin polar transport / gravitropism / root development / auxin-activated signaling pathway / vesicle membrane / lateral plasma membrane / response to light stimulus / cell surface / mitochondrion / plasma membrane
Similarity search - Function
Membrane transport protein / Auxin efflux carrier, plant type / Membrane transport protein
Similarity search - Domain/homology
2-(naphthalen-1-ylcarbamoyl)benzoic acid / Auxin efflux carrier component 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsSu, N.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
CitationJournal: Nature / Year: 2022
Title: Structures and mechanisms of the Arabidopsis auxin transporter PIN3.
Authors: Nannan Su / Aiqin Zhu / Xin Tao / Zhong Jie Ding / Shenghai Chang / Fan Ye / Yan Zhang / Cheng Zhao / Qian Chen / Jiangqin Wang / Chen Yu Zhou / Yirong Guo / Shasha Jiao / Sufen Zhang / Han ...Authors: Nannan Su / Aiqin Zhu / Xin Tao / Zhong Jie Ding / Shenghai Chang / Fan Ye / Yan Zhang / Cheng Zhao / Qian Chen / Jiangqin Wang / Chen Yu Zhou / Yirong Guo / Shasha Jiao / Sufen Zhang / Han Wen / Lixin Ma / Sheng Ye / Shao Jian Zheng / Fan Yang / Shan Wu / Jiangtao Guo /
Abstract: The PIN-FORMED (PIN) protein family of auxin transporters mediates polar auxin transport and has crucial roles in plant growth and development. Here we present cryo-electron microscopy structures of ...The PIN-FORMED (PIN) protein family of auxin transporters mediates polar auxin transport and has crucial roles in plant growth and development. Here we present cryo-electron microscopy structures of PIN3 from Arabidopsis thaliana in the apo state and in complex with its substrate indole-3-acetic acid and the inhibitor N-1-naphthylphthalamic acid (NPA). A. thaliana PIN3 exists as a homodimer, and its transmembrane helices 1, 2 and 7 in the scaffold domain are involved in dimerization. The dimeric PIN3 forms a large, joint extracellular-facing cavity at the dimer interface while each subunit adopts an inward-facing conformation. The structural and functional analyses, along with computational studies, reveal the structural basis for the recognition of indole-3-acetic acid and NPA and elucidate the molecular mechanism of NPA inhibition on PIN-mediated auxin transport. The PIN3 structures support an elevator-like model for the transport of auxin, whereby the transport domains undergo up-down rigid-body motions and the dimerized scaffold domains remain static.
History
DepositionJan 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Auxin efflux carrier component 3
A: Auxin efflux carrier component 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5504
Polymers147,9672
Non-polymers5832
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Auxin efflux carrier component 3 / AtPIN3


Mass: 73983.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PIN3, At1g70940, F15H11.14 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9S7Z8
#2: Chemical ChemComp-E7O / 2-(naphthalen-1-ylcarbamoyl)benzoic acid


Mass: 291.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H13NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: NPA-bound state of AtPIN3(AtPIN3-NPA) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293
Buffer solutionpH: 8
SpecimenConc.: 6 mg/ml / Embedding 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: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 554149 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036066
ELECTRON MICROSCOPYf_angle_d0.4818266
ELECTRON MICROSCOPYf_dihedral_angle_d4.568804
ELECTRON MICROSCOPYf_chiral_restr0.037990
ELECTRON MICROSCOPYf_plane_restr0.005998

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