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- EMDB-37376: Structure of AtHKT1;1 in NaCl at 2.7 Angstroms resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-37376
TitleStructure of AtHKT1;1 in NaCl at 2.7 Angstroms resolution
Map data
Sample
  • Complex: Structure of AtHKT1;1 in NaCl at 2.7 Angstroms resolution
    • Protein or peptide: Sodium transporter HKT1
  • Ligand: SODIUM ION
KeywordsHKT / salt tolerance / ion selectivity / TRANSPORT PROTEIN
Function / homology
Function and homology information


potassium ion transmembrane transporter activity / response to osmotic stress / sodium ion transport / response to salt stress / potassium ion transport / plasma membrane
Similarity search - Function
Potassium/sodium transporter Trk/HKT / : / Cation transporter / Cation transport protein
Similarity search - Domain/homology
Sodium transporter HKT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang J / Su N / Guo J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870724 China
CitationJournal: Mol Plant / Year: 2024
Title: Structures and ion transport mechanisms of plant high-affinity potassium transporters.
Authors: Jiangqin Wang / Yanping Luo / Fan Ye / Zhong Jie Ding / Shao Jian Zheng / Shuai Qiao / Yong Wang / Jiangtao Guo / Wei Yang / Nannan Su /
Abstract: Plant high-affinity K transporters (HKTs) mediate Na and K uptake, maintain Na/K homeostasis, and therefore play crucial roles in plant salt tolerance. In this study, we present cryoelectron ...Plant high-affinity K transporters (HKTs) mediate Na and K uptake, maintain Na/K homeostasis, and therefore play crucial roles in plant salt tolerance. In this study, we present cryoelectron microscopy structures of HKTs from two classes, class I HKT1;1 from Arabidopsis thaliana (AtHKT1;1) and class II HKT2;1 from Triticum aestivum (TaHKT2;1), in both Na- and K-bound states at 2.6- to 3.0-Å resolutions. Both AtHKT1;1 and TaHKT2;1 function as homodimers. Each HKT subunit consists of four tandem domain units (D1-D4) with a repeated K-channel-like M-P-M topology. In each subunit, D1-D4 assemble into an ion conduction pore with a pseudo-four-fold symmetry. Although both TaHKT2;1 and AtHKT1;1 have only one putative Na ion bound in the selectivity filter with a similar coordination pattern, the two HKTs display different K binding modes in the filter. TaHKT2;1 has three K ions bound in the selectivity filter, but AtHKT1;1 has only two K ions bound in the filter, which has a narrowed external entrance due to the presence of a Ser residue in the first filter motif. These structures, along with computational, mutational, and electrophysiological analyses, enable us to pinpoint key residues that are critical for the ion selectivity of HKTs. The findings provide new insights into the ion selectivity and ion transport mechanisms of plant HKTs and improve our understanding about how HKTs mediate plant salt tolerance and enhance crop growth.
History
DepositionSep 5, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37376.png

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Map

FileDownload / File: emd_37376.map.gz / Format: CCP4 / Size: 35.3 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.)
0.93 Å/pix.
x 210 pix.
= 195.3 Å		0.93 Å/pix.
x 210 pix.
= 195.3 Å		0.93 Å/pix.
x 210 pix.
= 195.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.12457835 - 0.1929329
Average (Standard dev.)0.00018174588 (±0.0063146297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 195.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37376_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_37376_half_map_2.map
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Sample components

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Entire : Structure of AtHKT1;1 in NaCl at 2.7 Angstroms resolution

EntireName: Structure of AtHKT1;1 in NaCl at 2.7 Angstroms resolution
Components
  • Complex: Structure of AtHKT1;1 in NaCl at 2.7 Angstroms resolution
    • Protein or peptide: Sodium transporter HKT1
  • Ligand: SODIUM ION

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Supramolecule #1: Structure of AtHKT1;1 in NaCl at 2.7 Angstroms resolution

SupramoleculeName: Structure of AtHKT1;1 in NaCl at 2.7 Angstroms resolution
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Sodium transporter HKT1

MacromoleculeName: Sodium transporter HKT1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 57.504965 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDRVVAKIAK IRSQLTKLRS LFFLYFIYFL FFSFLGFLAL KITKPRTTSR PHDFDLFFTS VSAITVSSMS TVDMEVFSNT QLIFLTILM FLGGEIFTSF LNLYVSYFTK FVFPHNKIRH ILGSYNSDSS IEDRCDVETV TDYREGLIKI DERASKCLYS V VLSYHLVT ...String:
MDRVVAKIAK IRSQLTKLRS LFFLYFIYFL FFSFLGFLAL KITKPRTTSR PHDFDLFFTS VSAITVSSMS TVDMEVFSNT QLIFLTILM FLGGEIFTSF LNLYVSYFTK FVFPHNKIRH ILGSYNSDSS IEDRCDVETV TDYREGLIKI DERASKCLYS V VLSYHLVT NLVGSVLLLV YVNFVKTARD VLSSKEISPL TFSVFTTVST FANCGFVPTN ENMIIFRKNS GLIWLLIPQV LM GNTLFPC FLVLLIWGLY KITKRDEYGY ILKNHNKMGY SHLLSVRLCV LLGVTVLGFL IIQLLFFCAF EWTSESLEGM SSY EKLVGS LFQVVNSRHT GETIVDLSTL SPAILVLFIL MMYLPPYTLF MPLTEQKTIE KEGGDDDSEN GKKVKKSGLI VSQL SFLTI CIFLISITER QNLQRDPINF NVLNITLEVI SAYGNVGFTT GYSCERRVDI SDGGCKDASY GFAGRWSPMG KFVLI IVMF YGRFKQFTAK SGRAWILYPS SS

UniProtKB: Sodium transporter HKT1

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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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 K2 QUANTUM (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87784
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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