8K66

Cryo-EM structure of Oryza sativa HKT2;1 at 2.5 angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into ion selectivity and transport mechanisms of Oryza sativa HKT2;1 and HKT2;2/1 transporters.

Wang, X.Shen, X.Qu, Y.Zhang, H.Wang, C.Yang, F.Shen, H.

(2024) Nat Plants 10: 633-644

  • DOI: https://doi.org/10.1038/s41477-024-01665-4
  • Primary Citation of Related Structures:  
    8K66, 8K69

  • PubMed 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 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.


  • Organizational Affiliation

    Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cation transporter HKT2;1
A, B
543Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: HKT21HKT1Os06g0701700LOC_Os06g48810
Membrane Entity: Yes 
UniProt
Find proteins for Q0D9S3 (Oryza sativa subsp. japonica)
Explore Q0D9S3 
Go to UniProtKB:  Q0D9S3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0D9S3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T7X
Query on T7X

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B]
Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
PC1
Query on PC1

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H [auth A],
K [auth B]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PTY
Query on PTY

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
L [auth B],
M [auth B]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
CLR
Query on CLR

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G [auth A],
P [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NA
Query on NA

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I [auth A],
J [auth A],
Q [auth B],
R [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary