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- EMDB-35085: Cryo-EM structure of Arabidopsis thaliana SOS1 in an occluded sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-35085
TitleCryo-EM structure of Arabidopsis thaliana SOS1 in an occluded state, with expanded TMD
Map data
Sample
  • Complex: Arabidopsis sodium/hydrogen exchanger 7 (SOS1), expand
    • Protein or peptide: Sodium/hydrogen exchanger 7
  • Ligand: HEXADECANE
KeywordsSodium/proton antiporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


sodium:proton antiporter activity / chloroplast envelope / regulation of reactive oxygen species metabolic process / sodium ion transport / potassium ion transmembrane transport / response to salt stress / response to reactive oxygen species / response to hydrogen peroxide / response to oxidative stress / plasma membrane
Similarity search - Function
Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Cyclic nucleotide-binding domain superfamily
Similarity search - Domain/homology
Sodium/hydrogen exchanger 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang Y / Zhao Y / Gao Y
Funding support China, 1 items
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, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35085.png

Downloads & links

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Map

FileDownload / File: emd_35085.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.519
Minimum - Maximum-1.4978474 - 2.4756749
Average (Standard dev.)-0.0028280015 (±0.065400615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35085_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35085_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis sodium/hydrogen exchanger 7 (SOS1), expand

EntireName: Arabidopsis sodium/hydrogen exchanger 7 (SOS1), expand
Components
  • Complex: Arabidopsis sodium/hydrogen exchanger 7 (SOS1), expand
    • Protein or peptide: Sodium/hydrogen exchanger 7
  • Ligand: HEXADECANE

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Supramolecule #1: Arabidopsis sodium/hydrogen exchanger 7 (SOS1), expand

SupramoleculeName: Arabidopsis sodium/hydrogen exchanger 7 (SOS1), expand
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Sodium/hydrogen exchanger 7

MacromoleculeName: Sodium/hydrogen exchanger 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 127.327891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTTVIDATMA YRFLEEATDS SSSSSSSKLE SSPVDAVLFV GMSLVLGIAS RHLLRGTRVP YTVALLVIGI ALGSLEYGAK HNLGKIGHG IRIWNEIDPE LLLAVFLPAL LFESSFSMEV HQIKRCLGQM VLLAVPGVLI STACLGSLVK VTFPYEWDWK T SLLLGGLL ...String:
MTTVIDATMA YRFLEEATDS SSSSSSSKLE SSPVDAVLFV GMSLVLGIAS RHLLRGTRVP YTVALLVIGI ALGSLEYGAK HNLGKIGHG IRIWNEIDPE LLLAVFLPAL LFESSFSMEV HQIKRCLGQM VLLAVPGVLI STACLGSLVK VTFPYEWDWK T SLLLGGLL SATDPVAVVA LLKELGASKK LSTIIEGESL MNDGTAIVVF QLFLKMAMGQ NSDWSSIIKF LLKVALGAVG IG LAFGIAS VIWLKFIFND TVIEITLTIA VSYFAYYTAQ EWAGASGVLT VMTLGMFYAA FARTAFKGDS QKSLHHFWEM VAY IANTLI FILSGVVIAE GILDSDKIAY QGNSWRFLFL LYVYIQLSRV VVVGVLYPLL CRFGYGLDWK ESIILVWSGL RGAV ALALS LSVKQSSGNS HISKETGTLF LFFTGGIVFL TLIVNGSTTQ FVLRLLRMDI LPAPKKRILE YTKYEMLNKA LRAFQ DLGD DEELGPADWP TVESYISSLK GSEGELVHHP HNGSKIGSLD PKSLKDIRMR FLNGVQATYW EMLDEGRISE VTANIL MQS VDEALDQVST TLCDWRGLKP HVNFPNYYNF LHSKVVPRKL VTYFAVERLE SACYISAAFL RAHTIARQQL YDFLGES NI GSIVINESEK EGEEAKKFLE KVRSSFPQVL RVVKTKQVTY SVLNHLLGYI ENLEKVGLLE EKEIAHLHDA VQTGLKKL L RNPPIVKLPK LSDMITSHPL SVALPPAFCE PLKHSKKEPM KLRGVTLYKE GSKPTGVWLI FDGIVKWKSK ILSNNHSLH PTFSHGSTLG LYEVLTGKPY LCDLITDSMV LCFFIDSEKI LSLQSDSTID DFLWQESALV LLKLLRPQIF ESVAMQELRA LVSTESSKL TTYVTGESIE IDCNSIGLLL EGFVKPVGIK EELISSPAAL SPSNGNQSFH NSSEASGIMR VSFSQQATQY I VETRARAI IFNIGAFGAD RTLHRRPSSL TPPRSSSSDQ LQRSFRKEHR GLMSWPENIY AKQQQEINKT TLSLSERAMQ LS IFGSMVN VYRRSVSFGG IYNNKLQDNL LYKKLPLNPA QGLVSAKSES SIVTKKQLET RKHACQLPLK GESSTRQNTM VES SDEEDE DEGIVVRIDS PSKIVFRNDL

UniProtKB: Sodium/hydrogen exchanger 7

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Macromolecule #2: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 2 / Number of copies: 6 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE / Hexadecane

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dsx

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31721

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