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Yorodumi- PDB-8jda: Cyro-EM structure of the Na+/H+ antipoter SOS1 from Arabidopsis t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jda | ||||||
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Title | Cyro-EM structure of the Na+/H+ antipoter SOS1 from Arabidopsis thaliana,class2 | ||||||
Components | Sodium/hydrogen exchanger 7 | ||||||
Keywords | MEMBRANE PROTEIN / Sodium / Proton | ||||||
Function / homology | Function and homology information potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / chloroplast envelope / regulation of reactive oxygen species metabolic process / sodium ion transport / potassium ion transmembrane transport / response to salt stress / response to reactive oxygen species / regulation of intracellular pH ...potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / chloroplast envelope / regulation of reactive oxygen species metabolic process / sodium ion transport / potassium ion transmembrane transport / response to salt stress / response to reactive oxygen species / regulation of intracellular pH / response to hydrogen peroxide / response to oxidative stress / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å | ||||||
Authors | Yang, G.H. / Zhang, Y.M. / Zhou, J.Q. / Jia, Y.T. / Xu, X. / Fu, P. / Wu, H.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Plants / Year: 2023 Title: Structural basis for the activity regulation of Salt Overly Sensitive 1 in Arabidopsis salt tolerance. Authors: Yanming Zhang / Jiaqi Zhou / Xuping Ni / Qinrui Wang / Yutian Jia / Xia Xu / Haoyang Wu / Peng Fu / Han Wen / Yan Guo / Guanghui Yang / Abstract: The plasma membrane Na/H exchanger Salt Overly Sensitive 1 (SOS1) is crucial for plant salt tolerance. Unlike typical sodium/proton exchangers, SOS1 contains a large cytoplasmic domain (CPD) that ...The plasma membrane Na/H exchanger Salt Overly Sensitive 1 (SOS1) is crucial for plant salt tolerance. Unlike typical sodium/proton exchangers, SOS1 contains a large cytoplasmic domain (CPD) that regulates Na/H exchange activity. However, the underlying modulation mechanism remains unclear. Here we report the structures of SOS1 from Arabidopsis thaliana in two conformations, primarily differing in CPD flexibility. The CPD comprises an interfacial domain, a cyclic nucleotide-binding domain-like domain (CNBD-like domain) and an autoinhibition domain. Through yeast cell-based Na tolerance test, we reveal the regulatory role of the interfacial domain and the activation role of the CNBD-like domain. The CPD forms a negatively charged cavity that is connected to the ion binding site. The transport of Na may be coupled with the conformational change of CPD. These findings provide structural and functional insight into SOS1 activity regulation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jda.cif.gz | 181.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jda.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jda_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8jda_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8jda_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 8jda_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/8jda ftp://data.pdbj.org/pub/pdb/validation_reports/jd/8jda | HTTPS FTP |
-Related structure data
Related structure data | 36076MC 8jd9C 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: 129015.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NHX7 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9LKW9 |
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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: Homodimer of AtSOS1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
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: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 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: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 427505 / Symmetry type: POINT |