+Open data
-Basic information
Entry | Database: PDB / ID: 8iwo | ||||||
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Title | The rice Na+/H+ antiporter SOS1 in an auto-inhibited state | ||||||
Components | OsSOS1 | ||||||
Keywords | MEMBRANE PROTEIN / Na+/H+ antiporter / salt stress / 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 / chloroplast envelope / potassium ion transmembrane transport / regulation of intracellular pH / plasma membrane Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å | ||||||
Authors | Zhang, X.Y. / Tang, L.H. / Zhang, C.R. / Nie, J.W. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iwo.cif.gz | 341.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iwo.ent.gz | 273.3 KB | Display | PDB format |
PDBx/mmJSON format | 8iwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iwo_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8iwo_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8iwo_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 8iwo_validation.cif.gz | 92.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/8iwo ftp://data.pdbj.org/pub/pdb/validation_reports/iw/8iwo | HTTPS FTP |
-Related structure data
Related structure data | 35775MC 8j2mC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 128064.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: SOS1 / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q5ICN3 #2: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SOS1 from Oryza Sativa / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Oryza sativa (Asian cultivated rice) |
Source (recombinant) | Organism: Schizosaccharomyces pombe (fission yeast) |
Buffer solution | pH: 6.5 |
Specimen | Conc.: 2.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: dev_3689: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138460 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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