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- PDB-8k69: Cryo-EM structure of Oryza sativa HKT2;2/1 at 2.3 angstrom -

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Basic information

Entry
Database: PDB / ID: 8k69
TitleCryo-EM structure of Oryza sativa HKT2;2/1 at 2.3 angstrom
ComponentsCation transporter HKT2;2
KeywordsTRANSPORT PROTEIN / HKT / K+ transporter / Channel
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / sodium ion transport / potassium ion transport / membrane
Similarity search - Function
: / Cation transporter / Cation transport protein
Similarity search - Domain/homology
CHOLESTEROL / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PHOSPHATIDYLETHANOLAMINE / Phosphatidylinositol / CHOLESTEROL HEMISUCCINATE / Cation transporter HKT2;2
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsWang, X. / Shen, X. / Qu, Y. / Wang, C. / Shen, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Plants / Year: 2024
Title: Structural insights into ion selectivity and transport mechanisms of Oryza sativa HKT2;1 and HKT2;2/1 transporters.
Authors: Xiaohui Wang / Xiaoshuai Shen / Yannan Qu / Heng Zhang / Chu Wang / Fan Yang / Huaizong Shen /
Abstract: Plant high-affinity K transporters (HKTs) play a pivotal role in maintaining the balance of Na and K ions in plants, thereby influencing plant growth under K-depleted conditions and enhancing ...Plant high-affinity K transporters (HKTs) play a pivotal role in maintaining the balance of Na and K ions in plants, thereby influencing plant growth under K-depleted conditions and enhancing tolerance to salinity stress. Here we report the cryo-electron microscopy structures of Oryza sativa HKT2;1 and HKT2;2/1 at overall resolutions of 2.5 Å and 2.3 Å, respectively. Both transporters adopt a dimeric assembly, with each protomer enclosing an ion permeation pathway. Comparison between the selectivity filters of the two transporters reveals the critical roles of Ser88/Gly88 and Val243/Gly243 in determining ion selectivity. A constriction site along the ion permeation pathway is identified, consisting of Glu114, Asn273, Pro392, Pro393, Arg525, Lys517 and the carboxy-terminal Trp530 from the neighbouring protomer. The linker between domains II and III adopts a stable loop structure oriented towards the constriction site, potentially participating in the gating process. Electrophysiological recordings, yeast complementation assays and molecular dynamics simulations corroborate the functional importance of these structural features. Our findings provide crucial insights into the ion selectivity and transport mechanisms of plant HKTs, offering valuable structural templates for developing new salinity-tolerant cultivars and strategies to increase crop yields.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cation transporter HKT2;2
B: Cation transporter HKT2;2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,22720
Polymers121,5462
Non-polymers7,68118
Water2,270126
1


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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cation transporter HKT2;2 / OsHKT2 / 2 / Cation transporter HKT2 / OsHKT2 / Po-OsHKT2


Mass: 60773.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: HKT2;2, HKT2 / Production host: Homo sapiens (human) / References: UniProt: Q93XI5

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Non-polymers , 7 types, 144 molecules

#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H50O4
#3: Chemical ChemComp-T7X / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H83O13P
#4: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#6: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: OsHKT2;2/1 dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa subsp. indica (long-grained rice)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 639952 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0057960
ELECTRON MICROSCOPYf_angle_d1.04410774
ELECTRON MICROSCOPYf_dihedral_angle_d22.6571304
ELECTRON MICROSCOPYf_chiral_restr0.1371264
ELECTRON MICROSCOPYf_plane_restr0.0051242

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