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- EMDB-50952: auxin transporter PIN8 as symmetric dimer (outward/outward) with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50952
Titleauxin transporter PIN8 as symmetric dimer (outward/outward) with 4-CPA bound in the outward binding state
Map data
Sample
  • Complex: auxin transporter PIN8 as symmetric dimer (outward/outward) with 4-CPA bound in the outward binding state
    • Protein or peptide: Auxin efflux carrier component 8
  • Ligand: 2-(4-chloranylphenoxy)ethanoic acid
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water
KeywordsAuxin transport / AEC family / BART superfamily / MEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / pollen development / auxin-activated signaling pathway / cell periphery / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Auxin efflux carrier, plant type / : / Membrane transport protein / Membrane transport protein
Similarity search - Domain/homology
Auxin efflux carrier component 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsUng KL / Stokes DL / Pedersen BP
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101000936European Union
Citation
Journal: bioRxiv / Year: 2024
Title: Transport of herbicides by PIN-FORMED auxin transporters.
Authors: Lukas Schulz / Kien Lam Ung / Sarah Koutnik-Abele / David L Stokes / Bjørn Panyella Pedersen / Ulrich Z Hammes /
Abstract: Auxins are a group of phytohormones that control plant growth and development . Their crucial role in plant physiology has inspired development of potent synthetic auxins that can be used as ...Auxins are a group of phytohormones that control plant growth and development . Their crucial role in plant physiology has inspired development of potent synthetic auxins that can be used as herbicides . Phenoxyacetic acid derivatives are a widely used group of auxin herbicides in agriculture and research. Despite their prevalence, the identity of the transporters required for distribution of these herbicides in plants is both poorly understood and the subject of controversial debate . Here we show that PIN-FORMED auxin transporters transport a range of phenoxyacetic acid herbicides across the membrane and we characterize the molecular determinants of this process using a variety of different substrates as well as protein mutagenesis to control substrate specificity. Finally, we present Cryo-EM structures of PIN8 with 2,4-dichlorophenoxyacetic acid (2,4-D) or 4-chlorophenoxyacetic acid (4-CPA) bound. These structures represent five key states from the transport cycle, allowing us to describe conformational changes associated with substrate binding and transport across the membrane. Overall, our results reveal that phenoxyacetic acid herbicides use the same export machinery as endogenous auxins and exemplify how transporter binding sites undergo transformations that dictate substrate specificity. These results enable development of novel synthetic auxins and for guiding precision breeding of herbicide resistant crop plants.
#1: Journal: Nat.Plants / Year: 2025
Title: Transport of phenoxyacetic acid herbicides by PIN-FORMED auxin transporters
Authors: Schulz L / Ung KL / Zuzic L / Koutnik-Abele S / Stokes DL / Pedersen BP / Hammes UZ
History
DepositionJul 9, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50952.png

Downloads & links

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Map

FileDownload / File: emd_50952.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 416 pix.
= 269.152 Å		0.65 Å/pix.
x 416 pix.
= 269.152 Å		0.65 Å/pix.
x 416 pix.
= 269.152 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.48388702 - 0.6783911
Average (Standard dev.)0.000009312925 (±0.011668779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 269.152 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50952_msk_1.map
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Histogram (log scale)

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Half map: #1

Fileemd_50952_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50952_half_map_2.map
Projections & Slices
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Sample components

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Entire : auxin transporter PIN8 as symmetric dimer (outward/outward) with ...

EntireName: auxin transporter PIN8 as symmetric dimer (outward/outward) with 4-CPA bound in the outward binding state
Components
  • Complex: auxin transporter PIN8 as symmetric dimer (outward/outward) with 4-CPA bound in the outward binding state
    • Protein or peptide: Auxin efflux carrier component 8
  • Ligand: 2-(4-chloranylphenoxy)ethanoic acid
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

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Supramolecule #1: auxin transporter PIN8 as symmetric dimer (outward/outward) with ...

SupramoleculeName: auxin transporter PIN8 as symmetric dimer (outward/outward) with 4-CPA bound in the outward binding state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 81 KDa

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Macromolecule #1: Auxin efflux carrier component 8

MacromoleculeName: Auxin efflux carrier component 8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 41.541039 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGISWLDIYH VVSATVPLYV SMTLGFLSAR HLKLFSPEQC AGINKFVAKF SIPLLSFQII SENNPFKMSP KLILSDILQK FLVVVVLAM VLRFWHPTGG RGGKLGWVIT GLSISVLPNT LILGMPILSA IYGDEAASIL EQIVVLQSLI WYTILLFLFE L NAARALPS ...String:
MGISWLDIYH VVSATVPLYV SMTLGFLSAR HLKLFSPEQC AGINKFVAKF SIPLLSFQII SENNPFKMSP KLILSDILQK FLVVVVLAM VLRFWHPTGG RGGKLGWVIT GLSISVLPNT LILGMPILSA IYGDEAASIL EQIVVLQSLI WYTILLFLFE L NAARALPS SGASLEHTGN DQEEANIEDE PKEEEDEEEV AIVRTRSVGT MKILLKAWRK LIINPNTYAT LIGIIWATLH FR LGWNLPE MIDKSIHLLS DGGLGMAMFS LGLFMASQSS IIACGTKMAI ITMLLKFVLG PALMIASAYC IRLKSTLFKV AIL QAALPQ GVVPFVFAKE YNLHPEIIST GVIFGMLIAL PTTLAYYFLL DLPGENLYFQ

UniProtKB: Auxin efflux carrier component 8

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Macromolecule #2: 2-(4-chloranylphenoxy)ethanoic acid

MacromoleculeName: 2-(4-chloranylphenoxy)ethanoic acid / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1IHP
Molecular weightTheoretical: 186.592 Da

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Macromolecule #3: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: DLP
Molecular weightTheoretical: 782.082 Da
Chemical component information

ChemComp-DLP:
1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
100.0 mMNaClSodium chloride
0.5 mMC10H16N2O8EDTA
0.006 %C47H88O22LMNG
0.0006 %C31H50O4Cholesterol hemisuccinate
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: The grid was glow-discharge at 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Wait 4 seconds after sample loading, Blotting time 4 seconds with blotting force of -1 before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 14665 / Average electron dose: 58.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8093919
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7qp9

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 135522
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC / Details: Cryosparc ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Cryosparc NU refinement
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7qp9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Overall B value: 103.2
Output model

PDB-9g0z:
auxin transporter PIN8 as symmetric dimer (outward/outward) with 4-CPA bound in the outward binding state

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