7CJS | pdb_00007cjs

structure of aquaporin

PDB DOI: https://doi.org/10.2210/pdb7CJS/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Oryza sativa Japonica Group
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2020-07-13 Released: 2021-11-03
Deposition Author(s): Saitoh, Y., Ma, J.F., Suga, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.273 (Depositor), 0.273 (DCC)
R-Value Work:
0.245 (Depositor), 0.244 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 34716344 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-26535-x
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 220.91 kDa
Atom Count: 14,182
Modeled Residue Count: 1,731
Deposited Residue Count: 2,032
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aquaporin NIP2-1	A, B, C, D, E A, B, C, D, E, F, G, H	254	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: NIP2-1, LSI1, SIIT1, Os02g0745100, LOC_Os02g51110, OJ1118_G04.16, OJ1734_E02.43, OsJ_008085 Membrane Entity: Yes
UniProt
Find proteins for Q6Z2T3 (Oryza sativa subsp. japonica) Explore Q6Z2T3 Go to UniProtKB: Q6Z2T3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6Z2T3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain GA [auth H] SDF format, chain V [auth D] MOL2 format, chain GA [auth H] MOL2 format, chain V [auth D] mmCIF format, chain GA [auth H] mmCIF format, chain V [auth D]	GA [auth H], V [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain GA [auth H] Focus chain V [auth D] Interactions & Density Focus chain GA [auth H] Focus chain V [auth D]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain EA [auth H] MOL2 format, chain T [auth D] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth H] mmCIF format, chain T [auth D] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth H]	EA [auth H], J [auth A], N [auth B], T [auth D]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain EA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain T [auth D] Interactions & Density Focus chain EA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain T [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Z [auth F] SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain FA [auth H] SDF format, chain CA [auth G] SDF format, chain BA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth F] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth F] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G]	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		Interactions Focus chain BA [auth G] Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Z [auth F]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain W [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain DA [auth H] SDF format, chain AA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth H] mmCIF format, chain AA [auth G]	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		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Y [auth F]