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- EMDB-35950: The truncated rice Na+/H+ antiporter SOS1 (1-976) in a constituti... -

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Basic information

Entry
Database: EMDB / ID: EMD-35950
TitleThe truncated rice Na+/H+ antiporter SOS1 (1-976) in a constitutively active state
Map data
Sample
  • Complex: OsSOS1-1t
    • Protein or peptide: Na+/H+ antiporter
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate
KeywordsNa+/H+ antiporter / cation:proton antiporter family 1 / membrane protein
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
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang XY / Tang LH / Zhang CR / Nie JW
Funding support China, 1 items
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, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35950.png

Downloads & links

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Map

FileDownload / File: emd_35950.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.158
Minimum - Maximum-0.35105345 - 0.59784144
Average (Standard dev.)0.00021797142 (±0.019259265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpen map

Fileemd_35950_additional_1.map
Annotationsharpen map
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Half map: #2

Fileemd_35950_half_map_1.map
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Half map: #1

Fileemd_35950_half_map_2.map
Projections & Slices
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Sample components

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Entire : OsSOS1-1t

EntireName: OsSOS1-1t
Components
  • Complex: OsSOS1-1t
    • Protein or peptide: Na+/H+ antiporter
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate

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Supramolecule #1: OsSOS1-1t

SupramoleculeName: OsSOS1-1t / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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Macromolecule #1: Na+/H+ antiporter

MacromoleculeName: Na+/H+ antiporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 116.560547 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString: MDNPEAEPDD AVLFVGVSLV LGIASRHLLR GTRVPYTVAL LVLGVALGSL EFGTKHGMGK LGAGIRIWAN INPDLLLAVF LPALLFESS FSMEIHQIKK CMAQMVLLAG PGVLISTFFL GSALKLTFPY NWNWKTSLLL GGLLSATDPV AVVALLKELG A SKKLSTII ...String:
MDNPEAEPDD AVLFVGVSLV LGIASRHLLR GTRVPYTVAL LVLGVALGSL EFGTKHGMGK LGAGIRIWAN INPDLLLAVF LPALLFESS FSMEIHQIKK CMAQMVLLAG PGVLISTFFL GSALKLTFPY NWNWKTSLLL GGLLSATDPV AVVALLKELG A SKKLSTII EGESLMNDGT AIVVYQLFYR MVLGRTFDAG SIIKFLSEVS LGAVALGLAF GIASVLWLGF IFNDTIIEIA LT LAVSYIA FFTAQDALEV SGVLTVMTLG MFYAAFAKTA FKGDSQQSLH HFWEMVAYIA NTLIFILSGV VIADGVLENN VHF ERHGAS WGFLLLLYVF VQISRILVVV ILYPLLRHFG YGLDLKEATI LVWAGLRGAV ALSLSLSVKR ASDAVQTHLK PVDG TMFVF FTGGIVFLTL IFNGSTTQFL LHLLGMDRLA ATKLRILNYT KYEMLNKALE AFGDLRDDEE LGPPADWVTV KKYIT CLND LDDEPVHPHA VSDRNDRMHT MNLRDIRVRL LNGVQAAYWG MLEEGRITQT TANILMRSVD EAMDLVPTQE LCDWKG LRS NVHFPNYYRF LQMSRLPRRL ITYFTVERLE SGCYICAAFL RAHRIARRQL HDFLGDSEVA RIVIDESNAE GEEARKF LE DVRVTFPQVL RVLKTRQVTY SVLTHLSEYI QNLQKTGLLE EKEMAHLDDA LQTDLKKFKR NPPLVKMPRV SDLLNTHP L VGALPAAMRD PLLSSTKETV KGHGTILYRE GSRPTGIWLV SIGVVKWTSQ RLSSRHSLDP ILSHGSTLGL YEVLIGKPY ICDMITDSVV HCFFIEAEKI EQLRQSDPSI EIFLWQESAL VVARLLLPMM FEKMATHELR VLITERSTMN IYIKGEEIEL EQNFIGILL EGFLKTKNQT LITPPGLLLP PNADLNLFGL ESSAINRIDY CYTAPSYQVE ARARILFVEI GRPEIEADLQ R SASLISQT LELPRTQSAA AENLYFQGLE WSHPQFEKGS GDYKDDDDKG SGWSHPQFEK LEDYKDDDDK HHHHHHHHHH

UniProtKB: Na+/H+ antiporter

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Macromolecule #2: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradeca...

MacromoleculeName: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate
type: ligand / ID: 2 / Number of copies: 2 / Formula: 46E
Molecular weightTheoretical: 635.853 Da
Chemical component information

ChemComp-46E:
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate

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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

Concentration2.7 mg/mL
BufferpH: 6.5
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 43851
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8iwo


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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