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- EMDB-38992: The structure of Oryza sativa HKT1;5 salt tolerant variant -

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Basic information

Entry
Database: EMDB / ID: EMD-38992
TitleThe structure of Oryza sativa HKT1;5 salt tolerant variant
Map data
Sample
  • Complex: Structure of OsHKT1;1
    • Protein or peptide: Sodium transporter HKT1.5,Soluble cytochrome b562
Keywordsdimer / transmembrane protein / sodium transporter / BRIL-fused / MEMBRANE PROTEIN
Function / homology
Function and homology information


metal ion transport / inorganic cation transmembrane transport / monoatomic cation transmembrane transporter activity / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
: / Cation transporter / Cation transport protein / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Sodium transporter HKT1.5 / Soluble cytochrome b562
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYang GH / Gao R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171188 China
CitationJournal: J Integr Plant Biol / Year: 2024
Title: Structural insights into the Oryza sativa cation transporters HKTs in salt tolerance.
Authors: Ran Gao / Yutian Jia / Xia Xu / Peng Fu / Jiaqi Zhou / Guanghui Yang /
Abstract: The high-affinity potassium transporters (HKTs), selectively permeable to either Na alone or Na/K, play pivotal roles in maintaining plant Na/K homeostasis. Although their involvement in salt ...The high-affinity potassium transporters (HKTs), selectively permeable to either Na alone or Na/K, play pivotal roles in maintaining plant Na/K homeostasis. Although their involvement in salt tolerance is widely reported, the molecular underpinnings of Oryza sativa HKTs remain elusive. In this study, we elucidate the structures of OsHKT1;1 and OsHKT2;1, representing two distinct classes of rice HKTs. The dimeric assembled OsHKTs can be structurally divided into four domains. At the dimer interface, a half-helix or a loop in the third domain is coordinated by the C-terminal region of the opposite subunit. Additionally, we present the structures of OsHKT1;5 salt-tolerant and salt-sensitive variants, a key quantitative trait locus associated with salt tolerance. The salt-tolerant variant of OsHKT1;5 exhibits enhanced Na transport capability and displays a more flexible conformation. These findings shed light on the molecular basis of rice HKTs and provide insights into their role in salt tolerance.
History
DepositionFeb 2, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38992.png

Downloads & links

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Map

FileDownload / File: emd_38992.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.0757115 - 2.962263
Average (Standard dev.)-0.00005174951 (±0.06286204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38992_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_38992_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of OsHKT1;1

EntireName: Structure of OsHKT1;1
Components
  • Complex: Structure of OsHKT1;1
    • Protein or peptide: Sodium transporter HKT1.5,Soluble cytochrome b562

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Supramolecule #1: Structure of OsHKT1;1

SupramoleculeName: Structure of OsHKT1;1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa (Asian cultivated rice)

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Macromolecule #1: Sodium transporter HKT1.5,Soluble cytochrome b562

MacromoleculeName: Sodium transporter HKT1.5,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Molecular weightTheoretical: 70.163039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SMSSLDATTP RYDEFKRIYH LFLFHAHPFW LQLLYFLFIS LLGFLMLKAL PMKTSMVPRP MDLDLIFTSV SATTVSSMV AVEMESFSNS QLLLITLLML LGGEVFTSIL GLYFTNAKYS SKMIARRQLA DLEDNWETLN DNLKVIEKAD N AAQVKDAL ...String:
MDYKDDDDKG SMSSLDATTP RYDEFKRIYH LFLFHAHPFW LQLLYFLFIS LLGFLMLKAL PMKTSMVPRP MDLDLIFTSV SATTVSSMV AVEMESFSNS QLLLITLLML LGGEVFTSIL GLYFTNAKYS SKMIARRQLA DLEDNWETLN DNLKVIEKAD N AAQVKDAL TKMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQAA AEQLKTTRNA YI QKYLERA RSTLSSASKT TTTRLLMFVV MGYHAVVHVA GYTAIVVYLS AVGGAGAVVA GKGISAHTFA IFTVVSTFAN CGF VPTNEG MVSFRSFPGL LLLVMPHVLL GNTLFPVFLR LAIAALERVT GWPELGELLI RRRRGGGEGY DHLLPSSRTR FLAL TVAVL VVAQLALFCA MEWGSDGLRG LTAGQKLVGA LFMAVNSRHS GEMVVDLSTV SSAVVVLYVV MMYLPPYTTF VPVQD KHQQ TGAQSGQEGS SSSSIWQKLL MSPLSCLAIF IVVICITERR QIADDPINYS VLNIVVEVIS AYGNVGFSTG YSCARQ VRP DGSCRDLWVG FSGKWSKQGK LTLMAVMFYG RLKKFSLHGG QAWKIEGSAW SHPQFEKGGG SGGGSGGSAW SHPQFEK

UniProtKB: Sodium transporter HKT1.5, Soluble cytochrome b562, Sodium transporter HKT1.5

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118956
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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