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- EMDB-38991: The structure of Oryza sativa HKT2;1 -

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Basic information

Entry
Database: EMDB / ID: EMD-38991
TitleThe structure of Oryza sativa HKT2;1
Map data
Sample
  • Complex: Structure of Oryza sativa HKT2;1
    • Protein or peptide: Cation transporter HKT2;1,Soluble cytochrome b562
Keywordssodium/potassium sympoter / homodomer / transmembrane protein / BRIL-fused / PLANT PROTEIN
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / sodium ion transport / electron transport chain / potassium ion transport / 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
Cation transporter HKT2;1 / Soluble cytochrome b562
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice) / Oryza sativa Indica Group x Oryza nivara (rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsYang GH / Gao R / Jia YT / Xu X / Fu P / Zhou JQ
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_38991.png

Downloads & links

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Map

FileDownload / File: emd_38991.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.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.419
Minimum - Maximum-1.851434 - 2.563478
Average (Standard dev.)0.0008170785 (±0.052033305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38991_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38991_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : Structure of Oryza sativa HKT2;1

EntireName: Structure of Oryza sativa HKT2;1
Components
  • Complex: Structure of Oryza sativa HKT2;1
    • Protein or peptide: Cation transporter HKT2;1,Soluble cytochrome b562

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Supramolecule #1: Structure of Oryza sativa HKT2;1

SupramoleculeName: Structure of Oryza sativa HKT2;1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa (Asian cultivated rice)

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Macromolecule #1: Cation transporter HKT2;1,Soluble cytochrome b562

MacromoleculeName: Cation transporter HKT2;1,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Indica Group x Oryza nivara (rice)
Molecular weightTheoretical: 70.030367 KDa
Recombinant expressionOrganism: Oryza sativa Indica Group (long-grained rice)
SequenceString: MDYKDDDDKG SMTSIYHDFI HNKLQSFGRI GRYFVNFVVL AHRFIALHIH PFWIQLSYFL LISILGSVLL MFLKPSNPEF RPGYIDMLF LSTSALTLSS LITIEMEVLS SSQIVVITLL MLLGGEVFVS FLGLMLARRQ LADLEDNWET LNDNLKVIEK A DNAAQVKD ...String:
MDYKDDDDKG SMTSIYHDFI HNKLQSFGRI GRYFVNFVVL AHRFIALHIH PFWIQLSYFL LISILGSVLL MFLKPSNPEF RPGYIDMLF LSTSALTLSS LITIEMEVLS SSQIVVITLL MLLGGEVFVS FLGLMLARRQ LADLEDNWET LNDNLKVIEK A DNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALKL ANEGKVKEAQ AAAEQLKTTR NA YIQKYLE RARSTWFLGF VVFSYFVVIH VAGFLLVLWY ISRVSSAKAP LKKKGINIAL FSFSVTVSSF ANVGLVPTNE NMA IFSKNP GLLLLFIGQI LAGNTLYPLF LRLLIWFLGK VTKLRELKLM IKNPEELQYD YLLPKLPTAF LASTVIGLMA SLVT LFGAV DWNSSVFDGL SSYQKIINAL FMAVNARHSG ENSIDCSLIA PAVLVLFIIL MYLPPSTTFA LSNGDEKTAN KKAKR KLGL VVQNLAFSQL ACISVFVIVA FITERSRLRN DPLNFSALNM IFEIISAYGN VGLSTGYSCS RLQKLHPGSI CQDKPY SLS GWWSDEGKLL LVFVMLYGRL KAFTKGTGEY WRLWGSAWSH PQFEKGGGSG GGSGGSAWSH PQFEK

UniProtKB: Cation transporter HKT2;1, Soluble cytochrome b562, Cation transporter HKT2;1

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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 (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: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192005
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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