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- EMDB-37377: structure of AtHKT1;1 in KCl at 2.8 Angstroms resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-37377
Titlestructure of AtHKT1;1 in KCl at 2.8 Angstroms resolution
Map data
Sample
  • Complex: structure of AtHKT1;1 in KCl at 2.8 Angstroms resolution
    • Protein or peptide: Sodium transporter HKT1
  • Ligand: POTASSIUM IONPotassium
KeywordsHKT / ion selectivity / salt tolerance / 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: 2.8 Å
AuthorsWang JQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870724 China
CitationJournal: To Be Published
Title: structure of AtHKT1;1 in KCl at 2.8 Angstroms resolution
Authors: Wang JQ
History
DepositionSep 5, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37377.png

Downloads & links

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Map

FileDownload / File: emd_37377.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: 0.02
Minimum - Maximum-0.093256265 - 0.15657051
Average (Standard dev.)0.00019628214 (±0.0056533213)
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_37377_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_37377_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : structure of AtHKT1;1 in KCl at 2.8 Angstroms resolution

EntireName: structure of AtHKT1;1 in KCl at 2.8 Angstroms resolution
Components
  • Complex: structure of AtHKT1;1 in KCl at 2.8 Angstroms resolution
    • Protein or peptide: Sodium transporter HKT1
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: structure of AtHKT1;1 in KCl at 2.8 Angstroms resolution

SupramoleculeName: structure of AtHKT1;1 in KCl at 2.8 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: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54018

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