Arabidopsis thaliana PIN-FORMED 3 (AtPIN3)

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Figure 1: Polar Auxin Transport. Image by Jen Valenzuela (CC-BY-NC)^[1].

PIN-FORMED (PIN)[1] proteins in plants are responsible for the polar transport [2] of plant hormone auxin alongside AUXIN TRANSPORTER PROTEIN 1 (AUX1) and ATP-BINDING CASSETTE (ABC) transporters^[2]. The polar transport of Auxin is crucial for proper plant growth and development. Auxin (IAAH) enters the cell through influx transporter or passes directly through the plasma membrane into the cytosol. Auxin dissociates to release a proton (H+) and anion (IAA-) in the cytoplasm due to higher pH. Due to its charge, it requires PIN proteins to carry it out of the cell. Once it reenters the apoplast it can bind to H again and it moves to the next cell^[1] (Figure 1).

In Arabidopsis thaliana There are 8 PIN proteins divided into two subfamilies – six long PINs (PIN1-PIN4, PIN6 and PIN7) and two short PINs (PIN 5 and PIN8) that localize in the plasma membrane and the endoplasmic reticulum respectively. AtPIN3 is a long PIN that shares at least 54% similarity with other long PINs^[2].

Function

Auxin and hence the PIN proteins are involved in many processes like embryogenesis, organogenesis, cell fate determination, and cell division. It also contributes to trophic responses like gravitropism and phototropism^[2].

Mutation of PIN genes or their improper localization may lead to many developmental defects like shorter roots, reduced number of lateral roots, root meristem collapse, defective columella cells, abnormal cotyledons and altered leaf venation^[2].

spinqualitylabelsall models apo state Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Structure AtPIN3 is its (7wks) is a homodimer with 10 transmembrane (TM1-TM10) domains each (Figure 2). Both the N and the C terminal of the protein lie on the extracellular side. The 10 TM domains are divided into two groups a scaffold domain (TM1–2 and 6–7) and a transport domain (TM3–5 and 8–10)[2]. Figure 2:The transmembrane domains and cytoplasmic domains of one chain represented in their proper confirmation and as a simplified diagram. Figure obtained from: Su, et.al.,(2022)[2].Figure 1F and 1G The helices 1, 2 and 7 of the scaffold domains are involved in dimerization through symmetric interactions with a surface area of 1516 Å. The tilted TM7 interacts with TM1, TM2 and TM7 of the other subunit through hydrophobic packaging. TM2 establishes hydrophobic packaging at the base of the dimer. This combined scaffold domain remains static and has the transport domain on either side of it[2].

Figure 3:A clip taken from the YouTube video entitled: "Structure and mechanism of the plant PIN-FORMED auxin transporter" Posted by NanionTechnologies.^[3] Time Stamp: 30:00 to 30:15

The transport domain is predicted to undergo up-down rigid-body motion in an elevator-like model (Figure 3). Two weak helices TM4 and TM9 break in the middle and cross and connect to each other as short loops. These may provide a substrate binding site and allow for confirmational changes during auxin transport. A solvent accessible pathway is present between the scaffold and the transport domain. This was suggested as the location for the (7xxb). The elevator model is supported by a structural alignment of PIN3 in its apo and IAA bound state, which shows a movement of the transport domain 2-3 Å towards the scaffold domain once IAA binds^[2].(Figure 4).

Figure 4:On the left, the local confirmation change observed between the structures of PIN3apo and PIN3IAA showing the change of state due to binding of IAA.Figure obtained from: Su, et. al.(2022)^[2]Figure 2I. On the right, an overall confirmation change observed in the transport domain created using TopMatch ^[4]

The protein has a cytosolic domain which is a cytosolic extension of . It contains an Amphiphilic helix (AH) and 3 beta-strands(β1-3). The loop between the AH and β3 has many phosphorylation sites that regulate the subcellular localization and transport activity of the protein^[2].

References

1. ↑ ^{1.0 1.1} Ha, M., Morrow, M., & Algiers, K. (n.d.). Auxin. Retrieved from LibreTexts Biology: https://bio.libretexts.org/Bookshelves/Botany/Botany_(Ha_Morrow_and_Algiers)/04%3A_Plant_Physiology_and_Regulation/4.04%3A_Hormones/4.4.01%3A_Auxin#title
2. ↑ ^{2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9} Su, N., Zhu, A., Tao, X. et al. Structures and mechanisms of the Arabidopsis auxin transporter PIN3. Nature 609, 616–621 (2022).DOI:https://doi.org/10.1038/s41586-022-05142-w
3. ↑ Posted by NanionTechnologies Speakers:Bjørn Panyella Pedersen and Ulrich Hammes. (2022). Structure and Mechanism of the plat PIN-FORMED auxin transporter. Retrieved from YouTube: https://www.youtube.com/watch?v=NPQK7T_UhrI
4. ↑ Sippl, & Wiederstein. (2020). Retrieved from TopMatch: https://topmatch.services.came.sbg.ac.at/index_jsmol.html?query=7xxb&qname=7xxb&target=7wks&tname=7wks

This web page was created for an assignment in Course BI3323-Aug2025 (Structural Biology), IISER, Pune