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- EMDB-36077: Cyro-EM structure of the Na+/H+ antipoter SOS1 from Arabidopsis t... -
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Open data
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Basic information
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Title | Cyro-EM structure of the Na+/H+ antipoter SOS1 from Arabidopsis thaliana,class1 | |||||||||
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![]() | Sodium / Proton / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
![]() | Yang GH / Zhang YM / Zhou JQ / Jia YT / Xu X / Fu P / Wu HY | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
Images | ![]() | 71 KB | ||
Filedesc metadata | ![]() | 4.9 KB | ||
Others | ![]() ![]() | 59.2 MB 59.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 816.4 KB | Display | ![]() |
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Full document | ![]() | 816 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jd9MC ![]() 8jdaC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36077_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36077_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Homodimer of AtSOS1
Entire | Name: Homodimer of AtSOS1 |
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Components |
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-Supramolecule #1: Homodimer of AtSOS1
Supramolecule | Name: Homodimer of AtSOS1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Na+/H+ antipoter SOS1 from Arabidopsis thaliana
Macromolecule | Name: Na+/H+ antipoter SOS1 from Arabidopsis thaliana / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 228696 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |