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- PDB-8y6m: The structure of Oryza sativa HKT2;1 -

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Basic information

Entry
Database: PDB / ID: 8y6m
TitleThe structure of Oryza sativa HKT2;1
ComponentsCation transporter HKT2;1,Soluble cytochrome b562
KeywordsPLANT PROTEIN / sodium/potassium sympoter / homodomer / transmembrane protein / BRIL-fused
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / inorganic cation transmembrane transport / 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 Indica Group x Oryza nivara (rice)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsYang, G.H. / Gao, R. / Jia, Y.T. / Xu, X. / Fu, P. / Zhou, J.Q.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cation transporter HKT2;1,Soluble cytochrome b562
B: Cation transporter HKT2;1,Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)140,0612
Polymers140,0612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cation transporter HKT2;1,Soluble cytochrome b562 / OsHKT2 / 1 / Cation transporter HKT1 / OsHKT1 / Po-OsHKT1 / Cytochrome b-562


Mass: 70030.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Indica Group x Oryza nivara (rice), (gene. exp.) Escherichia coli (E. coli)
Gene: HKT2;1, HKT1, OsI_023492, cybC
Production host: Oryza sativa Indica Group (long-grained rice)
References: UniProt: A2YGP9, UniProt: P0ABE7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of Oryza sativa HKT2;1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192005 / Symmetry type: POINT

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