7Y3E | pdb_00007y3e

Cryo-EM structure of Arabidopsis thaliana SOS1 in an occluded state

• PDB DOI: https://doi.org/10.2210/pdb7Y3E/pdb
• EM Map EMD-33592: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2022-06-10 Released: 2023-08-09 
• Deposition Author(s): Wang, Y., Zhao, Y., Gao, Y.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Architecture and autoinhibitory mechanism of the plasma membrane Na + /H + antiporter SOS1 in Arabidopsis.

Wang, Y., Pan, C., Chen, Q., Xie, Q., Gao, Y., He, L., Li, Y., Dong, Y., Jiang, X., Zhao, Y.

(2023) Nat Commun 14: 4487-4487

• PubMed: 37495621 
• DOI: https://doi.org/10.1038/s41467-023-40215-y
• Primary Citation Related Structures: 
  7Y3E, 8HYA


• PubMed 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 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.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.
College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
National Center for Technology Innovation of Saline-Alkali tolerant Rice/College of Coastal Agricultural Sciences, Guangdong Ocean University, 524088, Zhanjiang, China.
National Center for Technology Innovation of Saline-Alkali tolerant Rice/College of Coastal Agricultural Sciences, Guangdong Ocean University, 524088, Zhanjiang, China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. [e-mail].
State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China. [e-mail].
College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 255.56 kDa 
• Atom Count: 14,572 
• Modeled Residue Count: 1,856 
• Deposited Residue Count: 2,292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/hydrogen exchanger 7	A, B	1,146	Arabidopsis thaliana	Mutation(s): 0  Gene Names: SOS1 Membrane Entity: Yes
UniProt
Find proteins for Q9LKW9 (Arabidopsis thaliana) Explore Q9LKW9  Go to UniProtKB:  Q9LKW9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R16 (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	HEXADECANE C16 H34 DCAYPVUWAIABOU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Wang, Y., Zhao, Y., Gao, Y.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB37030304

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references
• Version 1.2: 2025-07-02
  Changes: Data collection, Structure summary