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- EMDB-37381: Structure of TaHKT2;1 in NaCl at 2.6 Angstroms resolution -

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Entry
Database: EMDB / ID: EMD-37381
TitleStructure of TaHKT2;1 in NaCl at 2.6 Angstroms resolution
Map data
Sample
  • Complex: Structure of TaHKT2;1 in NaCl at 2.6 Angstroms resolution
    • Protein or peptide: HKT2
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsHKT / salt tolerance / ion selectivity / TRANSPORT PROTEIN
Function / homology: / Cation transporter / Cation transport protein / metal ion transport / monoatomic cation transmembrane transporter activity / plasma membrane / Uncharacterized protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress) / Triticum aestivum (bread wheat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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_37381.png

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Map

FileDownload / File: emd_37381.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.16078208 - 0.19058372
Average (Standard dev.)0.00015658647 (±0.008718982)
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_37381_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_37381_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Structure of TaHKT2;1 in NaCl at 2.6 Angstroms resolution

EntireName: Structure of TaHKT2;1 in NaCl at 2.6 Angstroms resolution
Components
  • Complex: Structure of TaHKT2;1 in NaCl at 2.6 Angstroms resolution
    • Protein or peptide: HKT2
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Structure of TaHKT2;1 in NaCl at 2.6 Angstroms resolution

SupramoleculeName: Structure of TaHKT2;1 in NaCl at 2.6 Angstroms resolution
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: HKT2

MacromoleculeName: HKT2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 60.20059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHLFLTLVHS TMDRVKRFYQ DFIHIKLHSF SRISRYVVDS IVFIYRFVAL HVHPFWIQLS YFLAIAILGS VLLISLKPSN PEFSPPYID MLYLSTSALT VSGLSTVKME DLSSSQIVVL TLLMLVGGEI FVSLLGLMLR VNHQDMQDLP SVKISSVPVE L EVLDLANS ...String:
MHLFLTLVHS TMDRVKRFYQ DFIHIKLHSF SRISRYVVDS IVFIYRFVAL HVHPFWIQLS YFLAIAILGS VLLISLKPSN PEFSPPYID MLYLSTSALT VSGLSTVKME DLSSSQIVVL TLLMLVGGEI FVSLLGLMLR VNHQDMQDLP SVKISSVPVE L EVLDLANS MALCDESQLE DASHAIPPKK CTELKRSRSV KCLGYVVFGY FAVIHVLGFV LVFLYITHVP TASAPLNKKG IN IVLFSLS VTVASCANAG LVPTNENMVI FSKNSGLLLL LSGQMLAGNT LFPLFLRLLV WFLGKLTKVK ELRLMTKNPE EVH FANLLP RLPTVFLSST VIGIVAAGVT LFCSVDWNSS VFDGLGSYQK TVNAFFMVVN ARHSGENSID CSLMSPAIVV LFIG MMYLP SSATFAPPSG DTKTTNENTK GKGKRGSLVQ NLAFSPLGCN IIFVIVACIT ERRRLRSDPL NFSTLNMIFE VISAY GNVG LSTGYSCSRL HQLHPEIICQ DMPYSFSGWW SDGGKFLLVL VMLYGRLKVF AVSTGKSWKV

UniProtKB: Uncharacterized protein

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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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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47658
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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