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Yorodumi- PDB-7y9v: Structure of the auxin exporter PIN1 in Arabidopsis thaliana in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y9v | |||||||||||||||
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Title | Structure of the auxin exporter PIN1 in Arabidopsis thaliana in the IAA-bound state | |||||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN | |||||||||||||||
Function / homology | Function and homology information cotyledon morphogenesis / leaf formation / cotyledon development / shoot system development / leaf shaping / xylem and phloem pattern formation / auxin efflux transmembrane transporter activity / inflorescence development / auxin polar transport / gravitropism ...cotyledon morphogenesis / leaf formation / cotyledon development / shoot system development / leaf shaping / xylem and phloem pattern formation / auxin efflux transmembrane transporter activity / inflorescence development / auxin polar transport / gravitropism / plant-type cell wall / photomorphogenesis / root development / flower development / auxin-activated signaling pathway / embryo development ending in seed dormancy / plasmodesma / basal plasma membrane / apical part of cell / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) Escherichia coli (E. coli) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
Authors | Sun, L. / Liu, X. / Yang, Z. / Xia, J. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y9v.cif.gz | 181.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y9v.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 7y9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y9v_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7y9v_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7y9v_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 7y9v_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/7y9v ftp://data.pdbj.org/pub/pdb/validation_reports/y9/7y9v | HTTPS FTP |
-Related structure data
Related structure data | 33693MC 7y9tC 7y9uC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9C6B8 #2: Antibody | 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 | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250009 / Symmetry type: POINT |