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- PDB-8jd9: Cyro-EM structure of the Na+/H+ antipoter SOS1 from Arabidopsis t... -

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Basic information

Entry
Database: PDB / ID: 8jd9
TitleCyro-EM structure of the Na+/H+ antipoter SOS1 from Arabidopsis thaliana,class1
ComponentsSodium/hydrogen exchanger 7
KeywordsMEMBRANE 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
Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Cyclic nucleotide-binding domain superfamily
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sodium/hydrogen exchanger 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsYang, G.H. / Zhang, Y.M. / Zhou, J.Q. / Jia, Y.T. / Xu, X. / Fu, P. / Wu, H.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionMay 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/hydrogen exchanger 7
B: Sodium/hydrogen exchanger 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,6114
Polymers258,0312
Non-polymers1,5802
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium/hydrogen exchanger 7 / Na(+)/H(+) exchanger 7 / NHE-7 / Protein SALT OVERLY SENSITIVE 1


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
#2: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homodimer of AtSOS1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228696 / Symmetry type: POINT

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