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Yorodumi- PDB-8iab: The Arabidopsis CLCa transporter bound with chloride, ATP and PIP2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8iab | |||||||||
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Title | The Arabidopsis CLCa transporter bound with chloride, ATP and PIP2 | |||||||||
Components | Chloride channel protein CLC-a | |||||||||
Keywords | MEMBRANE PROTEIN / Transporter / ATP / PIP2 | |||||||||
Function / homology | Function and homology information nitrate transmembrane transport / nitrate transmembrane transporter activity / response to nitrate / voltage-gated chloride channel activity / chloride transport / chloride channel complex Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Yang, Z. / Zhang, X. / Zhang, P. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids. Authors: Zhao Yang / Xue Zhang / Shiwei Ye / Jingtao Zheng / Xiaowei Huang / Fang Yu / Zhenguo Chen / Shiqing Cai / Peng Zhang / Abstract: Chloride channels (CLCs) transport anion across membrane to regulate ion homeostasis and acidification of intracellular organelles, and are divided into anion channels and anion/proton antiporters. ...Chloride channels (CLCs) transport anion across membrane to regulate ion homeostasis and acidification of intracellular organelles, and are divided into anion channels and anion/proton antiporters. Arabidopsis thaliana CLCa (AtCLCa) transporter localizes to the tonoplast which imports NO and to a less extent Cl from cytoplasm. The activity of AtCLCa and many other CLCs is regulated by nucleotides and phospholipids, however, the molecular mechanism remains unclear. Here we determine the cryo-EM structures of AtCLCa bound with NO and Cl, respectively. Both structures are captured in ATP and PI(4,5)P bound conformation. Structural and electrophysiological analyses reveal a previously unidentified N-terminal β-hairpin that is stabilized by ATP binding to block the anion transport pathway, thereby inhibiting the AtCLCa activity. While AMP loses the inhibition capacity due to lack of the β/γ- phosphates required for β-hairpin stabilization. This well explains how AtCLCa senses the ATP/AMP status to regulate the physiological nitrogen-carbon balance. Our data further show that PI(4,5)P or PI(3,5)P binds to the AtCLCa dimer interface and occupies the proton-exit pathway, which may help to understand the inhibition of AtCLCa by phospholipids to facilitate guard cell vacuole acidification and stomatal closure. In a word, our work suggests the regulatory mechanism of AtCLCa by nucleotides and phospholipids under certain physiological scenarios and provides new insights for future study of CLCs. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iab.cif.gz | 250.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iab.ent.gz | 201.4 KB | Display | PDB format |
PDBx/mmJSON format | 8iab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iab_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8iab_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8iab_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 8iab_validation.cif.gz | 76.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/8iab ftp://data.pdbj.org/pub/pdb/validation_reports/ia/8iab | HTTPS FTP |
-Related structure data
Related structure data | 35299MC 8iadC 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: 85488.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CLC-A, CBSCLC5, At5g40890, MHK7.12 / Production host: Komagataella pastoris (fungus) / References: UniProt: P92941 #2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / Has ligand of interest | N | |
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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
Component | Name: The Arabidopsis CLCa transporter / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Source (recombinant) | Organism: Komagataella pastoris (fungus) |
Buffer solution | pH: 8 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 56.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135900 / Symmetry type: POINT |