+Open data
-Basic information
Entry | Database: PDB / ID: 7wks | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Apo state of AtPIN3 | |||||||||
Components | Auxin efflux carrier component 3 | |||||||||
Keywords | TRANSPORT PROTEIN / PIN-FORMED (PIN) protein | |||||||||
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 | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Su, N. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7wks.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7wks.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wks_validation.pdf.gz | 915.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7wks_full_validation.pdf.gz | 920.9 KB | Display | |
Data in XML | 7wks_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 7wks_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/7wks ftp://data.pdbj.org/pub/pdb/validation_reports/wk/7wks | HTTPS FTP |
-Related structure data
Related structure data | 32568MC 7wkwC 7xxbC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | 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 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: apo state AtPIN3(AtPIN3apo) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
Buffer solution | pH: 8 |
Specimen | Conc.: 6 mg/ml / 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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126203 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|