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- PDB-8j2m: The truncated rice Na+/H+ antiporter SOS1 (1-976) in a constituti... -

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Basic information

Entry
Database: PDB / ID: 8j2m
TitleThe truncated rice Na+/H+ antiporter SOS1 (1-976) in a constitutively active state
ComponentsNa+/H+ antiporter
KeywordsMEMBRANE PROTEIN / Na+/H+ antiporter / cation:proton antiporter family 1
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / potassium ion transmembrane transport / regulation of intracellular pH / plasma membrane
Similarity search - Function
Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Chem-46E / Na+/H+ antiporter
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang, X.Y. / Tang, L.H. / Zhang, C.R. / Nie, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2020YFA0509903 China
CitationJournal: Nat Plants / Year: 2023
Title: Structure and activation mechanism of the rice Salt Overly Sensitive 1 (SOS1) Na/H antiporter.
Authors: Xiang-Yun Zhang / Ling-Hui Tang / Jia-Wei Nie / Chun-Rui Zhang / Xiaonan Han / Qi-Yu Li / Li Qin / Mei-Hua Wang / Xiahe Huang / Feifei Yu / Min Su / Yingchun Wang / Rui-Ming Xu / Yan Guo / ...Authors: Xiang-Yun Zhang / Ling-Hui Tang / Jia-Wei Nie / Chun-Rui Zhang / Xiaonan Han / Qi-Yu Li / Li Qin / Mei-Hua Wang / Xiahe Huang / Feifei Yu / Min Su / Yingchun Wang / Rui-Ming Xu / Yan Guo / Qi Xie / Yu-Hang Chen /
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 ...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 in the unwound transmembrane helix 5 (TM), 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.
History
DepositionApr 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na+/H+ antiporter
B: Na+/H+ antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,3934
Polymers233,1212
Non-polymers1,2722
Water0
1


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

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Components

#1: Protein Na+/H+ antiporter / Os12g0641100 protein / Plasma membrane Na+/H+ antiporter / putative / expressed


Mass: 116560.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: SOS1, LOC_Os12g44360, Os12g0641100, OSNPB_120641100 / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q5ICN3
#2: Chemical ChemComp-46E / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate


Mass: 635.853 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H66NO8P
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: OsSOS1-1t / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Source (recombinant)Organism: Schizosaccharomyces pombe (fission yeast)
Buffer solutionpH: 6.5
SpecimenConc.: 2.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
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 FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3.23D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43851 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8IWO

8iwo


Accession code: 8IWO / Source name: PDB / Type: experimental model

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