7CJS

structure of aquaporin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for high selectivity of a rice silicon channel Lsi1.

Saitoh, Y.Mitani-Ueno, N.Saito, K.Matsuki, K.Huang, S.Yang, L.Yamaji, N.Ishikita, H.Shen, J.R.Ma, J.F.Suga, M.

(2021) Nat Commun 12: 6236-6236

  • DOI: https://doi.org/10.1038/s41467-021-26535-x
  • Primary Citation of Related Structures:  
    7CJS

  • PubMed Abstract: 

    Silicon (Si), the most abundant mineral element in the earth's crust, is taken up by plant roots in the form of silicic acid through Low silicon rice 1 (Lsi1). Lsi1 belongs to the Nodulin 26-like intrinsic protein subfamily in aquaporin and shows high selectivity for silicic acid. To uncover the structural basis for this high selectivity, here we show the crystal structure of the rice Lsi1 at a resolution of 1.8 Å. The structure reveals transmembrane helical orientations different from other aquaporins, characterized by a unique, widely opened, and hydrophilic selectivity filter (SF) composed of five residues. Our structural, functional, and theoretical investigations provide a solid structural basis for the Si uptake mechanism in plants, which will contribute to secure and sustainable rice production by manipulating Lsi1 selectivity for different metalloids.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science, Okayama University, Tsushima Naka 3-1-1, Kita, Okayama, 700-8530, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aquaporin NIP2-1
A, B, C, D, E
A, B, C, D, E, F, G, H
254Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: NIP2-1LSI1SIIT1Os02g0745100LOC_Os02g51110OJ1118_G04.16OJ1734_E02.43OsJ_008085
Membrane Entity: Yes 
UniProt
Find proteins for Q6Z2T3 (Oryza sativa subsp. japonica)
Explore Q6Z2T3 
Go to UniProtKB:  Q6Z2T3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6Z2T3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download Ideal Coordinates CCD File 
GA [auth H],
V [auth D]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
BOG
Query on BOG

Download Ideal Coordinates CCD File 
EA [auth H],
J [auth A],
N [auth B],
T [auth D]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
BA [auth G]
CA [auth G]
FA [auth H]
K [auth A]
L [auth A]
BA [auth G],
CA [auth G],
FA [auth H],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
R [auth C],
U [auth D],
X [auth E],
Z [auth F]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
I [auth A]
M [auth B]
Q [auth C]
AA [auth G],
DA [auth H],
I [auth A],
M [auth B],
Q [auth C],
S [auth D],
W [auth E],
Y [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.568α = 90
b = 92.453β = 102.14
c = 166.126γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description