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- PDB-8hya: Cryo-EM structure of Arabidopsis thaliana SOS1 in an occluded sta... -

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Basic information

Entry
Database: PDB / ID: 8hya
TitleCryo-EM structure of Arabidopsis thaliana SOS1 in an occluded state, with expanded TMD
ComponentsSodium/hydrogen exchanger 7
KeywordsMEMBRANE PROTEIN / Sodium/proton antiporter
Function / homology
Function and homology information


sodium:proton antiporter activity / chloroplast envelope / regulation of reactive oxygen species metabolic process / sodium ion transport / response to salt stress / potassium ion transmembrane transport / response to reactive oxygen species / response to hydrogen peroxide / response to oxidative stress / plasma membrane
Similarity search - Function
Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / Cyclic nucleotide-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXADECANE / Sodium/hydrogen exchanger 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang, Y. / Zhao, Y. / Gao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030304 China
CitationJournal: Nat Commun / Year: 2023
Title: Architecture and autoinhibitory mechanism of the plasma membrane Na/H antiporter SOS1 in Arabidopsis.
Authors: Yuhang Wang / Chengcai Pan / Qihao Chen / Qing Xie / Yiwei Gao / Lingli He / Yue Li / Yanli Dong / Xingyu Jiang / Yan Zhao /
Abstract: Salt-overly-sensitive 1 (SOS1) is a unique electroneutral Na/H antiporter at the plasma membrane of higher plants and plays a central role in resisting salt stress. SOS1 is kept in a resting state ...Salt-overly-sensitive 1 (SOS1) is a unique electroneutral Na/H antiporter at the plasma membrane of higher plants and plays a central role in resisting salt stress. SOS1 is kept in a resting state with basal activity and activated upon phosphorylation. Here, we report the structures of SOS1. SOS1 forms a homodimer, with each monomer composed of transmembrane and intracellular domains. We find that SOS1 is locked in an occluded state by shifting of the lateral-gate TM5b toward the dimerization domain, thus shielding the Na/H binding site. We speculate that the dimerization of the intracellular domain is crucial to stabilize the transporter in this specific conformation. Moreover, two discrete fragments and a residue W1013 are important to prevent the transition of SOS1 to an alternative conformational state, as validated by functional complementation assays. Our study enriches understanding of the alternate access model of eukaryotic Na/H exchangers.
History
DepositionJan 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Aug 9, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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)256,0148
Polymers254,6562
Non-polymers1,3596
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18740 Å2
ΔGint-156 kcal/mol
Surface area72000 Å2

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Components

#1: Protein Sodium/hydrogen exchanger 7 / Protein SALT OVERLY SENSITIVE 1


Mass: 127327.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOS1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9LKW9
#2: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34
Has ligand of interestN
Has protein modificationN

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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: Arabidopsis sodium/hydrogen exchanger 7 (SOS1), expand
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.5
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: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31721 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314888
ELECTRON MICROSCOPYf_angle_d0.63120160
ELECTRON MICROSCOPYf_dihedral_angle_d5.4542028
ELECTRON MICROSCOPYf_chiral_restr0.0412374
ELECTRON MICROSCOPYf_plane_restr0.0052472

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