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- EMDB-36076: Cyro-EM structure of the Na+/H+ antipoter SOS1 from Arabidopsis t... -

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Basic information

Entry
Database: EMDB / ID: EMD-36076
TitleCyro-EM structure of the Na+/H+ antipoter SOS1 from Arabidopsis thaliana,class2
Map data
Sample
  • Complex: Homodimer of AtSOS1
    • Protein or peptide: Na+/H+ antipoter SOS1 from Arabidopsis thaliana
KeywordsSodium / Proton / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / 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 / regulation of intracellular pH ...potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / 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 / regulation of intracellular pH / 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: 3.67 Å
AuthorsYang GH / Zhang YM / Zhou JQ / Jia YT / Xu X / Fu P / Wu HY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Plants / Year: 2023
Title: Structural basis for the activity regulation of Salt Overly Sensitive 1 in Arabidopsis salt tolerance.
Authors: Yanming Zhang / Jiaqi Zhou / Xuping Ni / Qinrui Wang / Yutian Jia / Xia Xu / Haoyang Wu / Peng Fu / Han Wen / Yan Guo / Guanghui Yang /
Abstract: The plasma membrane Na/H exchanger Salt Overly Sensitive 1 (SOS1) is crucial for plant salt tolerance. Unlike typical sodium/proton exchangers, SOS1 contains a large cytoplasmic domain (CPD) that ...The plasma membrane Na/H exchanger Salt Overly Sensitive 1 (SOS1) is crucial for plant salt tolerance. Unlike typical sodium/proton exchangers, SOS1 contains a large cytoplasmic domain (CPD) that regulates Na/H exchange activity. However, the underlying modulation mechanism remains unclear. Here we report the structures of SOS1 from Arabidopsis thaliana in two conformations, primarily differing in CPD flexibility. The CPD comprises an interfacial domain, a cyclic nucleotide-binding domain-like domain (CNBD-like domain) and an autoinhibition domain. Through yeast cell-based Na tolerance test, we reveal the regulatory role of the interfacial domain and the activation role of the CNBD-like domain. The CPD forms a negatively charged cavity that is connected to the ion binding site. The transport of Na may be coupled with the conformational change of CPD. These findings provide structural and functional insight into SOS1 activity regulation.
History
DepositionMay 2, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36076.png

Downloads & links

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Map

FileDownload / File: emd_36076.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.67
Minimum - Maximum-2.4324818 - 3.168813
Average (Standard dev.)0.0011684524 (±0.06513265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36076_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36076_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 : Homodimer of AtSOS1

EntireName: Homodimer of AtSOS1
Components
  • Complex: Homodimer of AtSOS1
    • Protein or peptide: Na+/H+ antipoter SOS1 from Arabidopsis thaliana

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Supramolecule #1: Homodimer of AtSOS1

SupramoleculeName: Homodimer of AtSOS1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Na+/H+ antipoter SOS1 from Arabidopsis thaliana

MacromoleculeName: Na+/H+ antipoter SOS1 from Arabidopsis thaliana / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MKLESSPVDA VLFVGMSLVL GIASRHLLRG TRVPYTVALL VIGIALGSLE YGAKHNLGKI GHGIRIWNEI DPELLLAVFL PALLFESSFS MEVHQIKRCL GQMVLLAVPG VLISTACLGS LVKVTFPYEW DWKTSLLLGG LLSATDPVAV VALLKELGAS KKLSTIIEGE ...String:
MKLESSPVDA VLFVGMSLVL GIASRHLLRG TRVPYTVALL VIGIALGSLE YGAKHNLGKI GHGIRIWNEI DPELLLAVFL PALLFESSFS MEVHQIKRCL GQMVLLAVPG VLISTACLGS LVKVTFPYEW DWKTSLLLGG LLSATDPVAV VALLKELGAS KKLSTIIEGE SLMNDGTAIV VFQLFLKMAM GQNSDWSSII KFLLKVALGA VGIGLAFGIA SVIWLKFIFN DTVIEITLTI AVSYFAYYTA QEWAGASGVL TVMTLGMFYA AFARTAFKGD SQKSLHHFWE MVAYIANTLI FILSGVVIAE GILDSDKIAY QGNSWRFLFL LYVYIQLSRV VVVGVLYPLL CRFGYGLDWK ESIILVWSGL RGAVALALSL SVKQSSGNSH ISKETGTLFL FFTGGIVFLT LIVNGSTTQF VLRLLRMDIL PAPKKRILEY TKYEMLNKAL RAFQDLGDDE ELGPADWPTV ESYISSLKGS EGELVHHPHN GSKIGSLDPK SLKDIRMRFL NGVQATYWEM LDEGRISEVT ANILMQSVDE ALDQVSTTLC DWRGLKPHVN FPNYYNFLHS KVVPRKLVTY FAVERLESAC YISAAFLRAH TIARQQLYDF LGESNIGSIV INESEKEGEE AKKFLEKVRS SFPQVLRVVK TKQVTYSVLN HLLGYIENLE KVGLLEEKEI AHLHDAVQTG LKKLLRNPPI VKLPKLSDMI TSHPLSVALP PAFCEPLKHS KKEPMKLRGV TLYKEGSKPT GVWLIFDGIV KWKSKILSNN HSLHPTFSHG STLGLYEVLT GKPYLCDLIT DSMVLCFFID SEKILSLQSD STIDDFLWQE SALVLLKLLR PQIFESVAMQ ELRALVSTES SKLTTYVTGE SIEIDCNSIG LLLEGFVKPV GIKEELISSP AALSPSNGNQ SFHNSSEASG IMRVSFSQQA TQYIVETRAR AIIFNIGAFG ADRTLHRRPS SLTPPRSSSS DQLQRSFRKE HRGLMSWPEN IYAKQQQEIN KTTLSLSERA MQLSIFGSMV NVYRRSVSFG GIYNNKLQDN LLYKKLPLNP AQGLVSAKSE SSIVTKKQLE TRKHACQLPL KGESSTRQNT MVESSDEEDE DEGIVVRIDS PSKIVFRNDL LESAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGSDYKDDD DK

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 427505
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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