8IWO | pdb_00008iwo

The rice Na+/H+ antiporter SOS1 in an auto-inhibited state

• PDB DOI: https://doi.org/10.2210/pdb8IWO/pdb
• EM Map EMD-35775: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Oryza sativa Japonica Group
• Expression System: Schizosaccharomyces pombe
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-03-30 Released: 2023-11-22 
• Deposition Author(s): Zhang, X.Y., Tang, L.H., Zhang, C.R., Nie, J.W., Chen, Y.H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.09 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure and activation mechanism of the rice Salt Overly Sensitive 1 (SOS1) Na + /H + antiporter.

Zhang, X.Y., Tang, L.H., Nie, J.W., Zhang, C.R., Han, X., Li, Q.Y., Qin, L., Wang, M.H., Huang, X., Yu, F., Su, M., Wang, Y., Xu, R.M., Guo, Y., Xie, Q., Chen, Y.H.

(2023) Nat Plants 9: 1924-1936

• PubMed: 37884653 
• DOI: https://doi.org/10.1038/s41477-023-01551-5
• Primary Citation Related Structures: 
  8IWO, 8J2M


• PubMed Abstract: 
  

  Salinity is one of the most severe abiotic stresses that adversely affect plant growth and agricultural productivity. The plant Na ⁺ /H ⁺ antiporter Salt Overly Sensitive 1 (SOS1) located in the plasma membrane extrudes excess Na ⁺ out of cells in response to salt stress and confers salt tolerance. However, the molecular mechanism underlying SOS1 activation remains largely elusive. Here we elucidate two cryo-electron microscopy structures of rice (Oryza sativa) SOS1, a full-length protein in an auto-inhibited state and a truncated version in an active state. The SOS1 forms a dimeric architecture, with an NhaA-folded transmembrane domain portion in the membrane and an elongated cytosolic portion of multiple regulatory domains in the cytoplasm. The structural comparison shows that SOS1 adopts an elevator transport mechanism accompanied by a conformational transition of the highly conserved Pro ¹⁴⁸ in the unwound transmembrane helix 5 (TM ₅ ), switching from an occluded conformation in the auto-inhibited state to a conducting conformation in the active state. These findings allow us to propose an inhibition-release mechanism for SOS1 activation and elucidate how SOS1 controls Na ⁺ homeostasis in response to salt stress.

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Organizational Affiliation: 
• State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
College of Grassland Science and Technology, China Agricultural University, Beijing, China.
State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China.
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
National Center of Technology Innovation for Maize, State Key Laboratory of Crop Germplasm Innovation and Molecular Breeding, Syngenta Group China, Beijing, China.
State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, 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.

Macromolecule Content 

• Total Structure Weight: 257.4 kDa 
• Atom Count: 15,118 
• Modeled Residue Count: 1,912 
• Deposited Residue Count: 2,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OsSOS1	A, B	1,148	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: SOS1 Membrane Entity: Yes
UniProt
Find proteins for Q5ICN3 (Oryza sativa subsp. japonica) Explore Q5ICN3  Go to UniProtKB:  Q5ICN3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
46E	C [auth A], D [auth B]	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate C33 H66 N O8 P NEZDNQCXEZDCBI-WJOKGBTCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.09 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Zhang, X.Y., Tang, L.H., Zhang, C.R., Nie, J.W., Chen, Y.H.

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Funding Organization	Location	Grant Number
Other government	China	2020YFA0509903

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary