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- PDB-7y9u: Structure of the auxin exporter PIN1 in Arabidopsis thaliana in t... -

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Basic information

Entry
Database: PDB / ID: 7y9u
TitleStructure of the auxin exporter PIN1 in Arabidopsis thaliana in the NPA-bound state
Components
  • Auxin efflux carrier component 1
  • nanobody
KeywordsTRANSPORT 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 / flower development / auxin polar transport / root development / plant-type cell wall / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-(naphthalen-1-ylcarbamoyl)benzoic 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: 3.3 Å
AuthorsSun, L. / Liu, X. / Yang, Z. / Xia, J.
Funding support China, 4items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020103 China
National Natural Science Foundation of China (NSFC)31900885 and 31870732 China
Other government2008085MC90 and 2008085J15 China
Other governmentWK9100000031 and YD9100002004 China
CitationJournal: Nature / Year: 2022
Title: Structural insights into auxin recognition and efflux by Arabidopsis PIN1.
Authors: Zhisen Yang / Jing Xia / Jingjing Hong / Chenxi Zhang / Hong Wei / Wei Ying / Chunqiao Sun / Lianghanxiao Sun / Yanbo Mao / Yongxiang Gao / Shutang Tan / Jiří Friml / Dianfan Li / Xin Liu / Linfeng Sun /
Abstract: Polar auxin transport is unique to plants and coordinates their growth and development. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and ...Polar auxin transport is unique to plants and coordinates their growth and development. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development.
History
DepositionJun 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)161,4846
Polymers160,9014
Non-polymers5832
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5830 Å2
ΔGint-32 kcal/mol
Surface area46770 Å2

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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 / Plasmid: pCAG / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9C6B8
#2: Antibody nanobody


Mass: 13369.910 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-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
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

Component
IDNameTypeEntity IDParent-IDSource
1AtPIN1 in complex with a nanobody and NPACOMPLEX#1-#20RECOMBINANT
2AtPIN1COMPLEX#11RECOMBINANT
3nanobodyCOMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Arabidopsis thaliana (thale cress)3702
32Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293F
32Escherichia coli (E. coli)562
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215094 / Symmetry type: POINT

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